[English] 日本語
Yorodumi
- PDB-4dv7: Crystal structure of the Thermus thermophilus 30S ribosomal subun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dv7
TitleCrystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, A915G, bound with streptomycin
Components
  • (ribosomal protein ...) x 20
  • 16S rRNA
KeywordsRIBOSOME/ANTIBIOTIC / decoding / Streptomycin / RNA structure / antibiotic resistance / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A ...Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / Ribosomal protein S14, type Z / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Few Secondary Structures / Irregular / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S17, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site
Similarity search - Domain/homology
STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.294 Å
AuthorsDemirci, H. / Murphy IV, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
CitationJournal: To be Published
Title: A structural basis for streptomycin resistance
Authors: Demirci, H. / Murphy IV, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
History
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S rRNA
B: ribosomal protein S2
C: ribosomal protein S3
D: ribosomal protein S4
E: ribosomal protein S5
F: ribosomal protein S6
G: ribosomal protein S7
H: ribosomal protein S8
I: ribosomal protein S9
J: ribosomal protein S10
K: ribosomal protein S11
L: ribosomal protein S12
M: ribosomal protein S13
N: ribosomal protein S14
O: ribosomal protein S15
P: ribosomal protein S16
Q: ribosomal protein S17
R: ribosomal protein S18
S: ribosomal protein S19
T: ribosomal protein S20
U: ribosomal protein THX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)791,761316
Polymers783,95221
Non-polymers7,809295
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)403.366, 403.366, 173.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S rRNA /


Mass: 494186.781 Da / Num. of mol.: 1 / Mutation: A915G / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: M26923.1

-
Ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein ribosomal protein S2 /


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371
#3: Protein ribosomal protein S3 /


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#4: Protein ribosomal protein S4 /


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#5: Protein ribosomal protein S5 /


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#6: Protein ribosomal protein S6 /


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#7: Protein ribosomal protein S7 /


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291
#8: Protein ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein ribosomal protein S9 /


Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374
#10: Protein ribosomal protein S10 /


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#11: Protein ribosomal protein S11 /


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376
#12: Protein ribosomal protein S12 /


Mass: 14966.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: F6DEQ7, UniProt: Q5SHN3*PLUS
#13: Protein ribosomal protein S13 /


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377
#14: Protein ribosomal protein S14 /


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: Protein ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#16: Protein ribosomal protein S16 /


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#17: Protein ribosomal protein S17 /


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: Protein ribosomal protein S18 /


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0
#19: Protein ribosomal protein S19 / 40S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#20: Protein ribosomal protein S20 /


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380
#21: Protein/peptide ribosomal protein THX / Ribosome


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

-
Non-polymers , 4 types, 702 molecules

#22: Chemical ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A / Streptomycin


Mass: 581.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H39N7O12 / Comment: medication, antibiotic*YM
#23: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 292 / Source method: obtained synthetically / Formula: Mg
#24: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#25: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.69 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 6.5 / Details: MPD, pH 6.5, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2010
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.294→35 Å / Num. all: 210955 / Num. obs: 210955 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.091 / Χ2: 1.126 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.294-3.424.60.875211410.95199.9
3.42-3.554.80.622210670.986199.7
3.55-3.724.80.422211311.041100
3.72-3.914.80.27211581.11199.9
3.91-4.164.80.186211871.156199.8
4.16-4.484.80.134211971.212199.7
4.48-4.934.80.102211961.213199.5
4.93-5.644.80.089211881.298198.9
5.64-7.094.70.082210901.374197.9
7.09-354.70.046206000.904193

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_978refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHENIXdev_978phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.294→34.924 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8533 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 10630 5.04 %FROM PDB ENTRY 2VQE
Rwork0.1677 ---
obs0.1698 210877 98.6 %-
all-210877 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 106.554 Å2 / ksol: 0.264 e/Å3
Displacement parametersBiso max: 495.91 Å2 / Biso mean: 161.2331 Å2 / Biso min: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1--13.3959 Å2-0 Å20 Å2
2---13.3959 Å20 Å2
3---11.1228 Å2
Refinement stepCycle: LAST / Resolution: 3.294→34.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19088 32508 334 407 52337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756233
X-RAY DIFFRACTIONf_angle_d1.02283506
X-RAY DIFFRACTIONf_chiral_restr0.0710400
X-RAY DIFFRACTIONf_plane_restr0.0064882
X-RAY DIFFRACTIONf_dihedral_angle_d18.28226010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.294-3.33170.35573600.30656240660093
3.3317-3.37080.3083360.27966777013100
3.3708-3.41190.34513840.276966737057100
3.4119-3.4550.2913600.262166837043100
3.455-3.50050.30243690.248966266995100
3.5005-3.54840.28523610.239467207081100
3.5484-3.5990.24643760.225266827058100
3.599-3.65270.24873550.21866887043100
3.6527-3.70970.27253730.209667207093100
3.7097-3.77040.2463790.199467047083100
3.7704-3.83540.25583140.193567357049100
3.8354-3.9050.20533530.180367057058100
3.905-3.980.22383450.17867367081100
3.98-4.06120.21863760.168867087084100
4.0612-4.14930.2043760.162766867062100
4.1493-4.24570.21293300.154667627092100
4.2457-4.35170.20993790.157966957074100
4.3517-4.46910.20253670.154267117078100
4.4691-4.60030.19823550.148467207075100
4.6003-4.74850.18493240.1456759708399
4.7485-4.91770.18343470.13986733708099
4.9177-5.11410.18173580.13436744710299
5.1141-5.3460.18153350.13696724705999
5.346-5.62680.19663610.13666708706999
5.6268-5.97770.19893330.14296713704698
5.9777-6.43660.18133340.14596723705798
6.4366-7.07950.18943490.13986675702497
7.0795-8.09270.19313350.1416682701797
8.0927-10.15430.18483730.15336678705196
10.1543-34.92590.21353330.1976237657087
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6250.043-0.20270.7498-0.04770.5981-0.002-0.0295-0.16830.25530.08130.1480.25520.0533-0.07830.82410.11450.06060.6885-0.01191.0629143.542883.4111-12.6372
23.9974-0.75490.44130.50980.11320.369-0.0392-2.13950.91090.41750.2259-0.3803-0.03090.1242-0.19111.2169-0.18830.01182.6243-0.83941.9368223.0032128.24969.8954
32.02770.766-0.80970.3763-0.48770.4766-0.1932-0.184-0.6373-0.11350.1866-0.52970.26640.18030.00361.20780.1773-0.02141.1956-0.06911.6102165.64770.7839-25.5518
42.94932.70020.50794.5274-2.08983.2905-0.90020.51730.03-1.28890.8694-2.0721-0.73780.59960.04161.4672-0.1330.54830.79910.18691.7153157.0513158.123-34.0532
56.63650.366-0.16235.4339-4.6663.9993-0.99710.94260.6068-2.7308-0.5283-1.640.41160.33811.51781.9805-0.13880.34081.16020.0461.5996153.4257150.8747-37.0363
68.66322.50076.16068.50632.77784.50960.3923-1.39470.0374-0.09650.05422.30140.4875-2.0807-0.33951.3724-0.20730.55620.8945-0.01522.5929148.7891159.972-20.5333
74.3729-2.86651.43057.06663.20997.1592-0.25710.190.0221-0.4625-0.6888-1.2201-0.24650.76940.91361.0646-0.13790.35841.26470.03291.6807165.6325162.9879-16.9831
84.97333.49582.90778.0816-1.64684.32610.0401-0.84430.73460.21770.8627-0.2403-0.91361.0621-0.8870.9657-0.11850.49841.2587-0.6361.6698175.1228156.3736-6.1747
95.3547-1.2016-1.23626.99451.72899.21880.00530.30141.21781.38281.532-2.3662-0.77182.9621-1.55091.6084-0.38420.29021.7776-0.90092.6635190.3539161.6757-4.1957
107.06974.06694.39645.35880.19424.56790.0308-0.39920.1607-0.26890.3296-0.6303-0.49390.7055-0.38841.02910.10110.56570.8786-0.22692.0647165.5318155.9974-12.2399
113.2284-3.85282.88.2263-2.50532.60190.4440.1584-0.1086-1.57470.3647-0.6261-0.36130.7326-0.74661.2788-0.15010.59170.7423-0.20881.9427159.0225150.0031-20.3604
124.4652-1.83421.6528.21864.62269.7288-0.47420.30110.4434-0.30020.4456-0.6277-2.13620.2852-0.03231.8777-0.25340.86140.7465-0.26812.4361158.4566167.8533-20.7531
131.25090.8924-0.89551.1279-1.36271.6992-0.2929-0.09790.53010.1030.73450.3439-0.55550.025-0.37063.7444-0.09980.6111.0157-0.19543.3599164.1546174.4584-22.5637
140.16120.00980.5040.0740.13471.69-0.0866-1.18870.49580.1549-0.01530.1256-0.4247-0.36710.06031.5505-0.03040.06824.6657-1.57222.104209.5741136.944628.3209
154.43222.51240.12674.9707-0.9038.20160.1641-2.55932.17131.1724-0.6561-0.5461-0.5460.15990.5041.6264-0.0353-0.13554.5623-1.13782.5496208.0627142.462136.0121
160.23960.2973-0.09440.75890.72942.68640.0782-0.3519-0.00640.7542-0.04070.26340.102-0.96030.09732.30420.1152-0.08795.2517-0.73491.2219198.7266137.92145.5049
170.01710.0279-0.04690.0825-0.21220.7799-0.3383-1.45030.85780.82510.06160.15630.1279-1.43060.44371.68010.0738-0.52473.7555-1.00031.6005199.7596141.717436.8734
183.81491.70470.56752.2094-1.52962.3825-0.2437-1.26390.37080.83811.1885-0.0754-0.0036-0.3639-0.88111.09980.13590.12682.9099-0.44621.3278188.5342130.420717.648
194.96344.8224-2.83678.5464-3.45153.6680.0185-0.8299-0.1680.1311-0.2665-1.57080.3574-0.06250.38880.91790.04260.10113.2771-1.0241.8598194.886130.610720.241
205.6633-5.9137-0.66826.19330.98575.2388-1.24111.4222-0.2691-0.3326-0.03781.62391.1882-0.82371.06562.0531-0.892-0.53851.5192-0.00171.5496155.0016105.271834.1889
216.3518-1.91446.3672.8254-4.19348.6674-0.3095-0.2956-0.38270.4036-0.65840.47490.68630.09840.91322.23670.78680.09071.4335-0.12321.1921151.7368115.052239.9888
222.13071.45771.3435.1827-0.52681.37261.0345-1.68891.08980.3959-0.6458-0.6537-0.12990.7941-0.41771.56040.1805-0.06881.4526-0.28980.9694159.0787112.708625.8813
236.07770.8123.52845.476-2.84375.71980.31-0.9557-0.06861.223-0.13120.44560.319-0.3711-0.18311.48430.10330.33440.7345-0.05420.9416134.2093105.401734.8692
248.7119-1.5569-6.48099.70551.09217.74151.10260.45751.2723-0.0964-0.17760.3062-2.3954-0.9912-0.92321.19820.2465-0.14160.89910.08080.8861136.8628113.608126.9308
255.8711-5.7944-4.87235.72674.81164.0631-0.4445-2.51751.64341.45050.4582-0.69130.26070.7774-0.07211.16350.07510.01251.7428-0.32751.1754164.6362125.12637.2784
264.8435-3.2653-4.92112.20323.3215.01910.4919-0.09590.33360.03490.2071-1.2729-0.65360.9513-0.65911.21460.0177-0.08731.5272-0.37861.7006185.469121.8876-2.731
273.4013-3.7912-3.26256.32751.465.4347-0.2697-0.66740.91270.31910.2348-0.293-0.4880.51810.13790.9346-0.30670.04181.2535-0.62741.286162.173129.045.0347
284.664-5.15645.55346.7087-5.76.7913-0.6882-0.49541.71190.75970.5854-1.3197-1.21540.30240.13641.4008-0.24810.19141.1104-0.31951.1973168.0337132.84265.8214
299.74576.3221-4.66558.5967-4.26062.57970.8607-1.31232.48051.00570.03272.0817-1.0219-0.0753-0.87420.71190.00780.24211.0585-0.18461.409145.4594129.06480.8667
302.55522.15611.7319.02184.39972.3726-1.36781.9371-3.3755-0.3502-0.41310.03881.8288-1.18361.66851.3068-0.17220.16971.15570.00431.3266152.7285119.7782-10.4684
318.1695-3.8798-4.71882.08922.12532.8051-1.1372-0.0344-0.35640.8139-0.07960.3052-0.0209-1.03211.25271.03590.13530.13790.7673-0.21011.2022145.722116.46041.0916
325.761-2.39960.8315.18642.70473.88570.1111-0.7689-0.06620.70020.12310.1283-0.01330.4705-0.24620.6367-0.16280.18070.861-0.1570.6055153.2788120.6543-0.465
337.6951-2.42183.71787.2308-4.90549.0631-0.3304-1.04090.93821.4787-0.38481.3367-1.1441-2.00420.56031.02150.17240.47641.0597-0.25461.1994135.9134134.3273-8.9173
344.50271.9011-5.43643.953-2.40676.5784-0.0621.0410.0767-0.220.4860.5677-1.16040.1104-0.35391.84990.2232-0.20392.35650.01740.8021168.1424117.1937-84.8396
353.95040.1336-2.79663.6752-1.45634.1652-1.27082.44910.1373-2.48230.3749-0.0310.7387-0.26470.8552.00380.13380.01381.8436-0.06190.6641176.5699113.445-97.5779
369.3946-2.56196.4633.4531.00947.27070.37640.81910.9296-0.6411-0.0438-0.1117-1.4218-0.5559-0.38512.02210.21230.30052.09520.34821.6866172.9422123.3182-90.6056
373.6514-2.0211.24994.89565.24389.80510.6131.11310.5945-1.57880.592-2.5635-0.42162.0698-1.12031.1135-0.05280.12862.15180.09991.5219190.5744117.821-83.2922
380.6118-0.05131.9073.3086-0.16486.061-0.75311.0161-0.4759-0.56790.1527-0.0187-0.6222-0.84320.6481.4370.28670.36551.97960.29460.7794172.1574119.4764-88.5371
392.15950.5281-1.62982.1005-1.19432.10880.9781-0.0389-0.76830.59620.52920.08631.0136-0.1196-1.37982.90030.08340.1971.3378-0.08231.1425169.2064106.4445-85.3635
406.1902-1.6971-0.6441.9930.42955.06980.27761.2762-1.3325-0.4721-1.4792-0.63080.82860.60761.19951.3240.17110.24151.78330.06911.6055177.995112.7779-85.8829
417.6703-1.07532.52749.88791.77069.9192-0.8507-0.16081.2734-1.7120.07442.2173-1.6996-0.90360.81491.47850.1424-0.2732.00720.9841.9474165.9744131.3633-73.4869
422.99241.87782.9657.11132.45023.0282-0.0469-0.04214.03971.1553-0.77062.4907-1.3662-0.04790.7081.5948-0.1354-0.12761.6509-0.28193.0366217.2844143.4561-21.7749
435.80333.1363-1.51346.6969-2.39596.3957-0.08820.87472.13740.1580.5605-0.1683-0.84160.714-0.48871.213-0.20750.59171.554-0.05873.0351244.5508146.0845-21.9806
447.02345.3496-2.16754.7895-1.98572.0214-0.37531.94651.0255-1.14171.3102-0.7199-1.73311-0.82781.4942-0.31780.35612.51830.83042.5428245.3761147.2402-35.951
458.8276.9648-6.47555.5711-5.51557.109-0.36421.71982.2371-0.52820.66390.68950.7186-0.3443-0.2851.33690.02410.04662.92310.09622.5265227.3536132.5226-37.7972
464.41690.03342.07810.180.76154.05080.2748-0.1072-0.64030.22950.4902-0.25141.46350.5531-0.70532.36790.6119-0.0322.50610.011.833220.0176125.4846-37.694
477.22364.9135-0.37253.63130.93334.91590.23840.46170.92360.05340.32670.1595-0.2244-0.589-0.53091.1757-0.39570.29351.68290.36032.7648236.2629136.4194-29.6847
484.11290.10092.30711.40970.6113.8815-0.20072.30460.432-1.10290.3458-1.44140.08762.4369-0.18271.1829-0.01780.6592.24790.21311.9847246.1417133.8598-33.9999
495.77831.4574.95832.16540.28384.7808-0.173-0.74270.64010.7905-0.00711.04430.4716-0.92260.21942.80720.42010.97772.27030.06131.8047220.2398126.538-44.8551
505.09876.17073.6569.45391.83666.16770.02090.1870.0399-0.9490.2693-0.4962-0.11510.5671-0.30190.71760.28740.3570.791-0.03941.0626140.0192126.3656-30.9135
517.07950.5412.08856.32320.78498.4831-0.16620.55431.4790.02220.42431.0336-0.9817-1.18-0.26830.62790.13040.18830.74410.26121.4509130.3575130.3044-31.1853
529.45290.10046.13151.54591.00158.3740.3201-0.72870.87430.96930.7986-0.2826-0.3961-0.4969-1.06281.24170.29720.44881.06960.10691.3737147.4704140.343-15.7453
530.29481.5140.23138.41951.31950.91820.2184-0.02620.16070.43850.1341-0.93350.112-0.0155-0.37460.83230.10230.02440.90890.04821.0826138.7327119.9418-21.1686
548.49317.2432-5.49156.2498-5.16146.5889-0.434-2.1572-0.39051.620.19520.61391.40010.84460.32561.25310.48840.74751.41530.14451.4765127.36111.9339-11.2289
555.14082.48484.43416.06083.63674.29570.0938-0.1492-0.46140.51180.25160.3946-0.20050.4886-0.33430.96690.10020.40230.99890.13011.0339129.4394119.6592-15.5388
568.56361.9834-2.01312.1705-2.56393.08360.4599-0.45570.80240.9036-0.47230.5161-0.2584-0.2705-0.05730.96720.23930.21510.83850.16031.1498126.8338118.551-17.3455
577.31837.57977.00578.22447.3556.73390.4558-0.50881.5644-1.40030.50760.0838-1.23950.3384-0.87261.81890.00880.18122.2496-1.36683.4258235.0549164.2406-0.6152
581.2412-2.189-0.79054.03520.7452.9303-0.13870.11670.7554-0.84750.8571-0.5348-0.44810.7915-0.54551.6575-0.4603-0.06671.8651-1.2844.0377245.5414167.0329-2.3214
593.92833.9145-3.84183.9246-3.61765.7768-0.24290.82963.8180.14870.21781.0692-1.58091.52090.051.4231-0.44090.542.2997-0.51044.8383249.8967155.8171-6.1533
602.57632.89151.67696.74944.64693.7993-0.36260.20550.0145-0.2691-0.05870.79780.227-0.47180.28741.85-0.8912-0.59241.5193-0.15443.9126241.0574160.9115-14.3619
611.1725-1.53050.82887.5377-5.18523.650.22340.15681.84170.71280.188-0.4749-0.18230.3799-0.38351.8505-0.5667-0.06121.9372-0.92183.3335242.6131166.8151-6.0769
623.02111.08170.25730.7784-0.00711.42120.5197-0.16761.1213-0.01060.13051.26450.0917-0.1855-0.37391.6437-0.33930.00991.4179-1.09614.8171236.1522163.7951-6.0731
631.9531-3.03641.54234.7712-2.09482.46270.0912-0.28861.79170.3202-0.9056-1.5046-0.4559-0.10160.83591.2206-0.24410.18932.0442-0.88263.3367227.0696154.2809-7.5031
642.9639-2.3979-2.13032.72730.1085.6957-0.4470.5489-0.4828-0.80520.89142.59740.859-1.0292-0.41011.0455-0.40760.01092.2067-0.28342.2803222.6074123.1046-7.2849
650.43580.0633-0.00620.0929-0.1130.1502-0.12610.5347-1.01060.74690.13370.26970.5136-0.0735-0.08091.7820.7299-0.22083.1223-1.80723.3797226.718155.193130.3806
668.225-0.73934.58680.76450.03744.358-0.3512-1.11131.28680.39640.4058-0.2227-0.2059-0.5868-0.02491.3818-0.08490.163.9779-1.99763.644217.4942161.111328.2364
671.43710.4668-1.1340.1604-0.43551.36410.2413-0.82930.6010.86590.4657-0.857-1.72530.3675-0.68122.47580.2665-0.21262.4727-1.9034.1265225.944166.055626.7067
681.10551.23531.10493.53141.64391.1823-0.6318-0.1793-0.44010.3797-0.64020.96480.4273-0.7351.16961.47380.17980.20123.3013-1.25383.1664225.404140.593918.5161
692.60590.5248-0.94162.06181.18435.59320.27630.0370.1206-0.6208-0.15850.0240.2233-0.6676-0.06551.3006-0.15050.28253.3451-0.86831.5982216.5931126.234710.2981
702.1902-1.2759-1.02194.2512-3.82926.04980.7016-0.68591.46312.688-1.2310.0293-0.274-0.63410.51631.889-0.0246-0.13722.8223-1.66553.0455225.9548156.314926.1778
712.2722-2.4501-1.3083.05170.95811.2540.63770.34160.33450.6928-0.46790.8653-0.315-0.6784-0.07462.51150.71670.30083.0972-1.80822.9999219.5649163.786338.3743
720.063-0.0059-0.01040.0528-0.09050.15980.4424-0.1676-1.5160.6645-0.6114-0.48071.06530.05160.11481.71190.1507-0.34042.2098-1.15163.5413228.1799154.302435.9785
735.3376-0.4509-2.95570.2515-0.60815.0561-0.0569-0.1745-0.1582-0.53540.16710.1550.61320.5272-0.09942.6065-0.51590.81482.46420.94411.6158221.6541120.1343-82.1897
745.4191-1.77686.46334.0505-3.522.0111-0.0077-0.30220.78010.25440.05070.1793-0.3222-0.1051-0.04830.88350.00480.38981.32120.07251.5719214.4535116.535-64.522
758.31532.1957-6.37842.4489-2.38279.60760.8123-0.48030.9256-0.3324-0.2607-1.0735-0.17651.6613-0.51821.09330.09480.23781.28750.15592.1649221.5507122.0689-64.806
766.98914.8331.27593.37761.21186.1567-1.23040.1865-0.2061-1.2364-0.5695-0.5188-0.11260.65741.70271.10020.10270.23711.44940.30911.4296210.713124.168-68.4093
774.981-3.59394.97439.3078-3.91065.002-0.29830.40592.98721.6966-0.5184-1.4044-2.5321.15780.79221.4117-0.2773-0.00991.2744-0.20111.8027213.6699129.4618-64.9318
780.02510.00910.00725.7631-3.01061.60760.3054-0.09210.157-0.0829-0.7382-0.41280.25590.55230.37441.12130.00110.33931.701-0.21781.3445195.3291112.8229-59.2346
796.70891.66196.17555.5217-2.40928.78220.05210.67810.29010.09280.2265-0.75420.02840.0994-0.31080.50810.1793-0.09480.919-0.07051.1452144.973999.3564-27.7481
807.979-7.44647.14636.9534-6.64516.35461.38291.1593-0.6999-1.5305-0.30220.31722.26661.3543-1.11761.14570.1738-0.28621.0207-0.19291.0659156.898184.5786-7.7712
818.63916.5838-1.39695.53060.23543.79920.0210.4555-0.57150.52150.1315-0.96910.5710.6971-0.08291.08510.3348-0.18651.12340.041.2121174.929377.79276.0145
825.91170.6877-2.15994.74811.16471.22210.4476-0.8334-0.64871.1780.0229-0.46711.13571.0416-0.52091.94870.157-0.43571.45120.16321.4565170.03681.235624.2349
837.1295-4.35013.24454.2447-4.16684.4756-0.0912-0.0035-0.8507-1.48270.1430.18792.35630.7773-0.05361.5980.22290.12432.0207-0.59792.1404274.7275116.4613-8.1198
846.99912.0901-1.85856.11-2.18613.81880.4126-1.40320.49260.2168-0.1566-0.08050.22730.4795-0.2660.80720.1757-0.13311.7732-0.36731.5023262.58111.13333.1636
858.58423.4478-5.54645.0381-4.47274.96230.4377-0.47590.2124-0.2895-0.94410.7467-0.8048-1.19170.5282.48890.2243-0.42923.7008-0.15761.5765219.8855114.545934.0779
860.56492.10660.68528.40872.84791.1757-0.4331-0.70420.33771.20290.23462.7229-0.1843-2.63560.15791.28730.190.12153.67210.50141.991232.4561116.985335.2264
870.0528-0.0158-0.01040.00510.00240.0030.22032.1346-1.1336-0.444-0.5793-0.2366-0.19350.18030.36641.2538-0.2725-0.15663.4559-0.90222.9386218.7527122.833728.7561
885.5062-1.8079-0.27012.52122.06322.0393-0.1708-1.40520.29461.46560.06660.6868-0.5897-0.28150.06862.8289-0.13120.79433.2323-0.81472.0115219.7351118.659123.3269
896.0155-6.9845-5.55998.67385.85115.7856-0.5644-0.11530.5560.967-0.43180.37680.5174-0.5520.97581.28620.038-0.11833.5395-0.8061.494222.3291129.108724.5814
908.15874.02066.70035.1640.94297.25360.36750.2853-0.59650.1333-0.17610.17010.22860.0503-0.09660.9744-0.35180.21523.4369-1.24521.5794212.2641129.931920.4782
916.1972.037-5.83551.7721-0.94096.35570.0587-0.3436-0.19350.00260.09910.13810.0339-0.155-0.14021.13510.3196-0.59532.4681-0.66632.5798215.2301140.530817.7491
924.31684.3285-3.74764.3448-3.76463.2634-0.70823.54130.9816-2.59250.862-0.0225-0.82870.0291-0.20111.64310.09790.17381.86280.22251.1427141.8333111.1082-74.1945
934.7281-4.5559-0.60294.46060.12946.11490.99351.59660.0288-0.9757-0.50480.4188-0.8822-0.7604-0.47141.0435-0.1261-0.16061.0820.25930.9297141.9994106.1397-66.6813
943.3339-4.2969-1.33685.9320.94752.30220.0284-2.802-0.9248-0.1340.5592-0.09230.30081.402-0.47040.82980.0635-0.14211.3050.00010.7412147.0259101.2382-58.0381
952.1915-0.43511.69048.2692.44632.2783-0.89620.5097-1.9862-0.2560.51491.25871.9515-1.90270.4161.3142-0.1896-0.11741.36510.22571.6065131.235498.2039-63.719
965.82051.40033.90170.36660.69864.32820.0208-0.3542-0.35780.54950.2240.05760.41360.2368-0.2231.58410.20250.41420.8740.20521.3521117.4476.230414.6646
975.25111.2456-0.18914.73252.7648.49830.22130.14940.620.44560.26390.25480.55130.0485-0.45631.2281-0.06720.37070.7780.05771.8203114.502876.81697.8628
987.92994.59474.67895.35685.49745.6401-0.2388-0.70281.23140.01570.4110.8773-0.9794-0.1031-0.06411.7288-0.05930.82220.85090.04591.6991110.817885.24521.5406
995.30744.0028-0.08243.50431.61127.0393-0.34910.2841.9218-1.1291-0.2748-0.3686-1.9237-0.59840.58471.27740.23430.24661.04340.52.5476100.533679.58274.801
1006.29313.74032.47666.50434.94557.11680.8488-0.5516-0.83271.0423-0.8289-0.16841.4843-0.22960.02271.8848-0.15710.69180.77350.15752.1782103.967973.195914.2982
1018.33536.76746.20466.59865.10044.6347-0.9887-0.7594-0.4959-0.1478-0.65231.09120.7385-1.17171.51112.1188-0.15010.8811.2725-0.14282.259193.609879.128615.5141
1023.13551.28972.32196.65496.17319.79260.25950.2255-0.198-0.34320.5081-0.1925-0.20620.1532-0.71280.6152-0.01540.04690.78690.29011.4075123.161583.9519-36.7009
1032.0342.98960.60965.77853.01543.5735-0.4308-0.28930.2471-0.49750.00940.46660.39550.41820.4220.65990.13370.01630.75570.20421.2073131.298790.2265-29.4063
1048.1789-3.99370.28633.6995-2.4133.02070.13070.40390.3905-0.7509-0.20690.768-0.0527-0.34820.12890.9712-0.1568-0.16020.99160.15681.3297117.112180.8883-39.1726
1056.6707-3.509-1.3478.5271-1.83755.80450.1380.1276-0.15790.20160.4326-0.13290.1221-0.0339-0.48340.9541-0.18980.03241.1431-0.02151.0505137.913885.915-44.8572
1068.0276-1.10055.54622.0244-0.92183.8437-0.2956-0.15120.9577-0.18590.3134-0.1986-1.6088-0.0082-0.02741.6478-0.14850.70591.376-0.10942.4551178.2243140.5983-67.3967
1079.2138-3.5581-6.23754.68225.03319.6965-0.71110.56680.4691-0.981-1.2662-0.345-0.74320.08941.78011.53330.4648-0.02732.16330.39571.3659172.937129.1397-76.8561
1082.46473.96253.32686.8846.08015.8313-0.21771.86632.47-2.0665-0.2691-1.3124-2.92921.26770.41531.18950.18940.46091.18680.59622.1667181.6719133.1597-74.7616
1095.6936-5.6182-5.91715.69495.90626.18610.10890.0321-0.2528-0.67770.9064-4.8317-0.51514.1494-0.92891.04960.09330.16191.7753-0.21531.5741187.0268128.4358-66.1529
1106.8612-0.3523-0.46458.00065.30273.52230.6372-1.20680.81540.19360.3332-0.4725-0.13851.9942-0.87951.92870.59120.69561.66590.12150.9921178.4425133.87-60.913
1115.6784-1.517-5.56453.84661.03215.52171.10160.2490.2982-0.2991-0.02080.6401-0.8318-0.2359-1.06681.1076-0.02580.05531.21190.10710.9231175.0648124.4559-69.09
1128.61132.5819-0.29615.6040.1893.415-0.0777-0.29350.1628-0.3636-0.0699-1.12450.44060.63530.12251.40990.35060.2411.48540.2661.314192.2853125.3584-71.7592
1131.88762.16022.67623.74040.47719.0642-0.5702-0.3528-0.0361-0.83460.12120.83931.9081-2.99690.30342.29470.7386-0.94453.1063-1.46552.4409252.4515111.858228.0298
1144.99080.84833.25339.1863-0.58882.2763-1.7357-1.08261.30521.76550.0364-0.1125-0.7068-0.24811.59232.02350.7528-0.41993.84320.23271.8667249.661295.945537.5273
1153.34060.75643.70710.65041.41634.8098-0.4432-1.98710.7441-0.1092-1.22974.46880.5488-4.33941.64961.8699-1.216-0.60233.89470.13383.2026257.11999.36132.8727
1166.1172-2.0059-0.89031.9527-0.03710.9449-0.0890.5856-0.62940.4321-0.2254-0.8180.63120.46420.28521.81810.48540.19023.41280.03252.2024249.282392.192830.5781
1170.1016-0.0152-0.01780.0080.00290.00070.074-0.0064-0.4099-0.24470.1555-0.1270.1161-0.2001-0.24741.91830.0094-0.18133.62170.17952.4441242.977890.158125.987
1189.73630.34387.09620.3329-0.14165.68920.7437-0.4546-1.2030.0439-0.4613-1.35790.51991.4904-0.31.62120.3195-0.37573.40150.28842.7379249.167596.331620.4936
1195.08151.27415.21352.67931.71225.29880.0207-0.1146-0.11010.12090.37360.41320.64110.2674-0.38351.1797-0.06960.30.56770.08771.2755113.272841.3165-16.0184
1209.71510.48711.97575.4412-2.19412.30360.4537-1.24340.02810.2867-0.32282.24861.7434-0.8777-0.19351.2313-0.05770.22270.90890.47621.5828100.476845.1302-25.4834
1212.9924-0.29533.63964.51524.11338.983-0.79290.93450.6339-0.4257-0.2320.26290.20.26360.89061.2173-0.37420.14941.22990.63561.918399.680950.0999-35.5487
1227.8048-5.23333.70854.2248-0.53797.05960.6850.0489-1.2020.2728-0.09731.59790.8609-0.8087-0.55911.5724-0.48820.06322.1783-0.46412.5932251.8462124.4063.0835
1238.8525-3.44723.16343.4838-4.38665.8117-0.1994-0.81472.00320.49910.16130.1901-1.41620.34320.05311.80260.1162-0.31091.3408-0.61672.392249.2437130.18284.3578
1245.64542.60263.53152.85970.87492.6201-0.6570.520.07320.13880.2681-0.5538-0.68740.63290.30982.144-0.9447-0.11463.0076-1.29992.3421253.3787131.422711.2715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)A5 - 920
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)A921 - 1400
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1544)A0
4X-RAY DIFFRACTION4chain 'B' and (resseq 7:25)B7 - 25
5X-RAY DIFFRACTION5chain 'B' and (resseq 26:43)B26 - 43
6X-RAY DIFFRACTION6chain 'B' and (resseq 44:62)B44 - 62
7X-RAY DIFFRACTION7chain 'B' and (resseq 63:87)B63 - 87
8X-RAY DIFFRACTION8chain 'B' and (resseq 88:122)B88 - 122
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:149)B123 - 149
10X-RAY DIFFRACTION10chain 'B' and (resseq 150:170)B150 - 170
11X-RAY DIFFRACTION11chain 'B' and (resseq 171:207)B171 - 207
12X-RAY DIFFRACTION12chain 'B' and (resseq 208:226)B208 - 226
13X-RAY DIFFRACTION13chain 'B' and (resseq 227:240)B227 - 240
14X-RAY DIFFRACTION14chain 'C' and (resseq 2:50)C2 - 50
15X-RAY DIFFRACTION15chain 'C' and (resseq 51:66)C51 - 66
16X-RAY DIFFRACTION16chain 'C' and (resseq 67:93)C67 - 93
17X-RAY DIFFRACTION17chain 'C' and (resseq 94:112)C94 - 112
18X-RAY DIFFRACTION18chain 'C' and (resseq 113:181)C113 - 181
19X-RAY DIFFRACTION19chain 'C' and (resseq 182:207)C182 - 207
20X-RAY DIFFRACTION20chain 'D' and (resseq 2:14)D2 - 14
21X-RAY DIFFRACTION21chain 'D' and (resseq 15:34)D15 - 34
22X-RAY DIFFRACTION22chain 'D' and (resseq 35:68)D35 - 68
23X-RAY DIFFRACTION23chain 'D' and (resseq 69:175)D69 - 175
24X-RAY DIFFRACTION24chain 'D' and (resseq 176:209)D176 - 209
25X-RAY DIFFRACTION25chain 'E' and (resseq 5:16)E5 - 16
26X-RAY DIFFRACTION26chain 'E' and (resseq 17:27)E17 - 27
27X-RAY DIFFRACTION27chain 'E' and (resseq 28:50)E28 - 50
28X-RAY DIFFRACTION28chain 'E' and (resseq 51:63)E51 - 63
29X-RAY DIFFRACTION29chain 'E' and (resseq 64:79)E64 - 79
30X-RAY DIFFRACTION30chain 'E' and (resseq 80:86)E80 - 86
31X-RAY DIFFRACTION31chain 'E' and (resseq 87:103)E87 - 103
32X-RAY DIFFRACTION32chain 'E' and (resseq 104:141)E104 - 141
33X-RAY DIFFRACTION33chain 'E' and (resseq 142:154)E142 - 154
34X-RAY DIFFRACTION34chain 'F' and (resseq 1:10)F1 - 10
35X-RAY DIFFRACTION35chain 'F' and (resseq 11:33)F11 - 33
36X-RAY DIFFRACTION36chain 'F' and (resseq 34:47)F34 - 47
37X-RAY DIFFRACTION37chain 'F' and (resseq 48:56)F48 - 56
38X-RAY DIFFRACTION38chain 'F' and (resseq 57:68)F57 - 68
39X-RAY DIFFRACTION39chain 'F' and (resseq 69:81)F69 - 81
40X-RAY DIFFRACTION40chain 'F' and (resseq 82:92)F82 - 92
41X-RAY DIFFRACTION41chain 'F' and (resseq 93:101)F93 - 101
42X-RAY DIFFRACTION42chain 'G' and (resseq 2:11)G2 - 11
43X-RAY DIFFRACTION43chain 'G' and (resseq 12:53)G12 - 53
44X-RAY DIFFRACTION44chain 'G' and (resseq 54:68)G54 - 68
45X-RAY DIFFRACTION45chain 'G' and (resseq 69:78)G69 - 78
46X-RAY DIFFRACTION46chain 'G' and (resseq 79:92)G79 - 92
47X-RAY DIFFRACTION47chain 'G' and (resseq 93:110)G93 - 110
48X-RAY DIFFRACTION48chain 'G' and (resseq 111:144)G111 - 144
49X-RAY DIFFRACTION49chain 'G' and (resseq 145:156)G145 - 156
50X-RAY DIFFRACTION50chain 'H' and (resseq 1:29)H1 - 29
51X-RAY DIFFRACTION51chain 'H' and (resseq 30:63)H30 - 63
52X-RAY DIFFRACTION52chain 'H' and (resseq 64:73)H64 - 73
53X-RAY DIFFRACTION53chain 'H' and (resseq 74:96)H74 - 96
54X-RAY DIFFRACTION54chain 'H' and (resseq 97:102)H97 - 102
55X-RAY DIFFRACTION55chain 'H' and (resseq 103:116)H103 - 116
56X-RAY DIFFRACTION56chain 'H' and (resseq 117:138)H117 - 138
57X-RAY DIFFRACTION57chain 'I' and (resseq 2:13)I2 - 13
58X-RAY DIFFRACTION58chain 'I' and (resseq 14:32)I14 - 32
59X-RAY DIFFRACTION59chain 'I' and (resseq 33:40)I33 - 40
60X-RAY DIFFRACTION60chain 'I' and (resseq 41:52)I41 - 52
61X-RAY DIFFRACTION61chain 'I' and (resseq 53:69)I53 - 69
62X-RAY DIFFRACTION62chain 'I' and (resseq 70:88)I70 - 88
63X-RAY DIFFRACTION63chain 'I' and (resseq 89:119)I89 - 119
64X-RAY DIFFRACTION64chain 'I' and (resseq 120:128)I120 - 128
65X-RAY DIFFRACTION65chain 'J' and (resseq 3:12)J3 - 12
66X-RAY DIFFRACTION66chain 'J' and (resseq 13:27)J13 - 27
67X-RAY DIFFRACTION67chain 'J' and (resseq 28:42)J28 - 42
68X-RAY DIFFRACTION68chain 'J' and (resseq 43:47)J43 - 47
69X-RAY DIFFRACTION69chain 'J' and (resseq 48:62)J48 - 62
70X-RAY DIFFRACTION70chain 'J' and (resseq 63:78)J63 - 78
71X-RAY DIFFRACTION71chain 'J' and (resseq 79:94)J79 - 94
72X-RAY DIFFRACTION72chain 'J' and (resseq 95:100)J95 - 100
73X-RAY DIFFRACTION73chain 'K' and (resseq 11:15)K11 - 15
74X-RAY DIFFRACTION74chain 'K' and (resseq 16:57)K16 - 57
75X-RAY DIFFRACTION75chain 'K' and (resseq 58:75)K58 - 75
76X-RAY DIFFRACTION76chain 'K' and (resseq 76:90)K76 - 90
77X-RAY DIFFRACTION77chain 'K' and (resseq 91:107)K91 - 107
78X-RAY DIFFRACTION78chain 'K' and (resseq 108:126)K108 - 126
79X-RAY DIFFRACTION79chain 'L' and (resseq 5:12)L5 - 12
80X-RAY DIFFRACTION80chain 'L' and (resseq 13:32)L13 - 32
81X-RAY DIFFRACTION81chain 'L' and (resseq 33:101)L33 - 101
82X-RAY DIFFRACTION82chain 'L' and (resseq 102:128)L102 - 128
83X-RAY DIFFRACTION83chain 'M' and (resseq 2:14)M2 - 14
84X-RAY DIFFRACTION84chain 'M' and (resseq 15:119)M15 - 119
85X-RAY DIFFRACTION85chain 'N' and (resseq 2:11)N2 - 11
86X-RAY DIFFRACTION86chain 'N' and (resseq 12:21)N12 - 21
87X-RAY DIFFRACTION87chain 'N' and (resseq 22:26)N22 - 26
88X-RAY DIFFRACTION88chain 'N' and (resseq 27:31)N27 - 31
89X-RAY DIFFRACTION89chain 'N' and (resseq 32:40)N32 - 40
90X-RAY DIFFRACTION90chain 'N' and (resseq 41:50)N41 - 50
91X-RAY DIFFRACTION91chain 'N' and (resseq 51:61)N51 - 61
92X-RAY DIFFRACTION92chain 'O' and (resseq 2:15)O2 - 15
93X-RAY DIFFRACTION93chain 'O' and (resseq 16:44)O16 - 44
94X-RAY DIFFRACTION94chain 'O' and (resseq 45:73)O45 - 73
95X-RAY DIFFRACTION95chain 'O' and (resseq 74:88)O74 - 88
96X-RAY DIFFRACTION96chain 'P' and (resseq 1:16)P1 - 16
97X-RAY DIFFRACTION97chain 'P' and (resseq 17:39)P17 - 39
98X-RAY DIFFRACTION98chain 'P' and (resseq 40:52)P40 - 52
99X-RAY DIFFRACTION99chain 'P' and (resseq 53:61)P53 - 61
100X-RAY DIFFRACTION100chain 'P' and (resseq 62:76)P62 - 76
101X-RAY DIFFRACTION101chain 'P' and (resseq 77:83)P77 - 83
102X-RAY DIFFRACTION102chain 'Q' and (resseq 2:28)Q2 - 28
103X-RAY DIFFRACTION103chain 'Q' and (resseq 29:45)Q29 - 45
104X-RAY DIFFRACTION104chain 'Q' and (resseq 46:81)Q46 - 81
105X-RAY DIFFRACTION105chain 'Q' and (resseq 82:100)Q82 - 100
106X-RAY DIFFRACTION106chain 'R' and (resseq 19:28)R19 - 28
107X-RAY DIFFRACTION107chain 'R' and (resseq 29:36)R29 - 36
108X-RAY DIFFRACTION108chain 'R' and (resseq 37:43)R37 - 43
109X-RAY DIFFRACTION109chain 'R' and (resseq 44:52)R44 - 52
110X-RAY DIFFRACTION110chain 'R' and (resseq 53:59)R53 - 59
111X-RAY DIFFRACTION111chain 'R' and (resseq 60:75)R60 - 75
112X-RAY DIFFRACTION112chain 'R' and (resseq 76:88)R76 - 88
113X-RAY DIFFRACTION113chain 'S' and (resseq 2:12)S2 - 12
114X-RAY DIFFRACTION114chain 'S' and (resseq 13:39)S13 - 39
115X-RAY DIFFRACTION115chain 'S' and (resseq 40:44)S40 - 44
116X-RAY DIFFRACTION116chain 'S' and (resseq 45:52)S45 - 52
117X-RAY DIFFRACTION117chain 'S' and (resseq 53:61)S53 - 61
118X-RAY DIFFRACTION118chain 'S' and (resseq 62:81)S62 - 81
119X-RAY DIFFRACTION119chain 'T' and (resseq 8:46)T8 - 46
120X-RAY DIFFRACTION120chain 'T' and (resseq 47:75)T47 - 75
121X-RAY DIFFRACTION121chain 'T' and (resseq 76:106)T76 - 106
122X-RAY DIFFRACTION122chain 'U' and (resseq 2:8)U2 - 8
123X-RAY DIFFRACTION123chain 'U' and (resseq 9:14)U9 - 14
124X-RAY DIFFRACTION124chain 'U' and (resseq 15:25)U15 - 25

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more