[English] 日本語
Yorodumi
- PDB-4nxn: Crystal Structure of the 30S ribosomal subunit from a GidB (RsmG)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nxn
TitleCrystal Structure of the 30S ribosomal subunit from a GidB (RsmG) mutant of Thermus thermophilus (HB8), bound with streptomycin
Components
  • (ribosomal protein ...) x 20
  • 16S rRNA
KeywordsRIBOSOME/ANTIBIOTIC / Streptomycin / RNA structure / antibiotic resistance / decoding / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / 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 S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Few Secondary Structures / Irregular / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S2, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site
Similarity search - Domain/homology
STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 ...STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / 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 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: 3.544 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
DepositionDec 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

-
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)790,490265
Polymers783,92121
Non-polymers6,570244
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)403.064, 403.064, 173.452
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: 494154.719 Da / Num. of mol.: 1 / 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: A0A0M9AFS9*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
#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: A0A0N0BLP2*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: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*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, 504 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.: 241 / 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.: 260 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence details30S RIBOSOMAL SUBUNIT IS FROM A GIDB (RSMG) MUTANT OF THERMUS THERMOPHILUS HB8.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, pH 6.5, VAPOR DIFFUSION, 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
ReflectionRedundancy: 3.3 % / Number: 557180 / Rmerge(I) obs: 0.092 / Χ2: 1.05 / D res high: 3.55 Å / D res low: 35 Å / Num. obs: 170381 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.623596.810.040.9993.1
6.067.6299.110.0631.0143.2
5.36.0699.610.0821.0193.3
4.825.399.710.1031.0693.3
4.474.8299.710.1311.0653.3
4.214.4799.710.1781.0923.3
44.2199.610.2491.0813.3
3.82499.510.3341.0863.3
3.683.8299.310.4781.0663.3
3.553.6899.110.6911.0283.3
ReflectionResolution: 3.535→35 Å / Num. all: 170381 / Num. obs: 170381 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.535-3.68199.1
3.68-3.82199.3
7.62-35196.8
3.82-4199.5
4-4.21199.6
4.21-4.47199.7
4.47-4.82199.7
4.82-5.3199.7
5.3-6.06199.6
6.06-7.62199.1

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXdev_1555refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.544→34.742 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7977 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 8517 5 %FROM PDB ENTRY 2VQE
Rwork0.1925 ---
obs0.1944 170277 99.17 %-
all-170277 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 517.03 Å2 / Biso mean: 148.0393 Å2 / Biso min: 15.27 Å2
Refinement stepCycle: LAST / Resolution: 3.544→34.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19088 32506 283 260 52137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556084
X-RAY DIFFRACTIONf_angle_d0.76283152
X-RAY DIFFRACTIONf_chiral_restr0.03710401
X-RAY DIFFRACTIONf_plane_restr0.0044882
X-RAY DIFFRACTIONf_dihedral_angle_d16.78125996
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 (%)
3.544-3.58430.35742940.31375219551398
3.5843-3.62640.33812720.30945342561499
3.6264-3.67060.32932880.29935324561299
3.6706-3.7170.32653010.29285328562999
3.717-3.76580.30313100.27055308561899
3.7658-3.81740.30432390.27095391563099
3.8174-3.87180.28292880.25925361564999
3.8718-3.92960.29312780.254253455623100
3.9296-3.99090.25212810.242554095690100
3.9909-4.05620.2922960.237853215617100
4.0562-4.1260.26583040.238553615665100
4.126-4.20090.27232800.220953655645100
4.2009-4.28160.26222490.222754145663100
4.2816-4.36880.25123100.21253565666100
4.3688-4.46360.24933080.21453855693100
4.4636-4.56730.23012920.198954105702100
4.5673-4.68120.22282580.191154235681100
4.6812-4.80750.24782670.19454235690100
4.8075-4.94850.20762930.184454135706100
4.9485-5.10780.22622740.183254095683100
5.1078-5.28970.22892710.177554315702100
5.2897-5.50070.21082840.169354115695100
5.5007-5.750.22712870.172354305717100
5.75-6.05170.20612660.1755456572299
6.0517-6.42860.20582730.17565461573499
6.4286-6.92140.21422830.16845450573399
6.9214-7.61130.20632980.16045438573699
7.6113-8.69750.1912830.15695457574098
8.6975-10.90150.18632810.15165466574797
10.9015-34.74340.20293090.16295453576294
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.64810.1194-0.23380.7926-0.05310.4835-0.003-0.0792-0.08570.28970.0780.14820.19510.0745-0.07671.12260.12590.01321.0011-0.03541.2614143.529883.4178-12.5364
24.965-1.02620.47470.640.18210.4143-0.1296-2.31160.88110.37510.3212-0.3779-0.0740.0293-0.14521.3503-0.18450.03062.6984-0.81071.8618222.9044128.27729.994
31.69070.8897-0.86970.4094-0.54590.2183-0.2882-0.1101-0.8157-0.10450.2828-0.64410.28890.1481-0.0121.42030.1636-0.03671.4127-0.03921.8053163.611268.9131-25.3727
40.6684-0.3537-0.09270.3440.1520.2043-0.0235-1.8829-2.59340.55530.21130.0967-0.28092.5809-0.30371.7823-0.2496-0.25795.0020.80643.5401204.1608110.7702-33.0346
52.20492.94550.39564.8698-0.86752.2243-0.57320.04130.0233-1.35690.6642-1.6161-1.0550.6632-0.10941.8929-0.08110.34061.26190.23822.1135157.0665157.826-34.1164
64.96691.19664.41858.60875.14056.4404-0.1318-0.27450.7108-0.5804-0.54551.158-0.0217-1.23820.66921.3845-0.05760.49010.96680.05311.9631150.9756156.0688-27.0795
78.99750.2319-2.87375.14161.56137.4151-0.15160.21120.4952-0.6087-0.3291-1.2234-1.17192.1120.42751.2286-0.14650.39051.28480.13291.8985167.7905162.1441-18.5174
87.0861-0.04331.58756.3754-3.12787.2933-0.0021-0.85660.78940.450.4884-0.2831-1.01611.3629-0.41911.2439-0.37150.58511.4814-0.6431.974174.6708156.8796-6.3736
96.4642-3.2979-2.52784.87363.04195.1281-0.0381-0.14341.11110.85221.6648-2.6254-0.40392.245-1.64831.8144-0.53050.10431.987-0.68192.6585190.8332161.6244-3.9716
102.95720.05892.1512.838-1.14995.98760.4158-0.00960.4438-0.75530.653-0.7604-0.930.4914-1.01651.3719-0.08470.67970.943-0.27712.2224160.9985156.1626-18.0619
112.75762.8676-1.17344.4201-2.67351.9699-0.1369-0.0221.0427-0.18530.5897-0.2641-1.1110.1172-0.5153.7975-0.3730.62391.5228-0.26043.223164.1222174.4034-22.3828
120.1751-0.335-0.12060.7110.1080.205-0.2847-1.88470.45120.56050.3531-0.0713-0.5779-0.3038-0.09441.8710.10350.03614.699-1.25021.9998205.1297138.607134.8335
131.3336-0.10080.88186.0132-1.21551.8712-0.2343-1.5619-0.13120.67410.6165-0.16940.1298-0.1885-0.41391.26020.00690.1563.1811-0.58851.7033190.1651130.384218.4296
149.3337-4.9953-2.69443.3288-0.77798.388-0.1285-0.5925-0.31771.19040.5868-0.0439-0.8293-0.3239-0.42671.88840.0547-0.09861.46620.00331.4163152.9673111.275337.6734
151.99130.41410.09836.5313-2.67391.15770.4336-0.93250.84060.6548-0.1939-0.4701-0.5610.6704-0.23071.6060.1078-0.01341.4914-0.34211.0336159.594113.061225.6134
163.74420.38632.60954.8864-5.11898.01720.4453-0.2401-0.19020.5601-0.04910.070.4787-0.0093-0.35421.68440.13040.26431.046-0.17771.3517135.1426103.945830.6801
172.4466-1.01072.3619.4678-2.69348.8788-0.3499-1.89480.37652.81930.52751.2923-1.1766-1.1914-0.15861.98680.29320.48291.7247-0.12281.3334130.756110.324147.2066
183.8384-1.6937-5.05664.08681.87626.84570.93940.57331.2923-0.0162-0.2793-0.2087-1.7392-0.8442-0.51951.57290.12340.03691.22550.0981.2074138.967114.070123.0348
192.5782-3.3938-3.89178.61662.35947.7834-0.221-1.08931.02091.5450.4459-0.27190.20110.9361-0.23570.99570.0138-0.06451.7983-0.45771.3963162.0598126.35058.449
209.2171-1.9326-7.19913.8532.97549.48310.17180.2476-0.67090.1965-0.55250.1608-0.5383-0.56960.39311.1535-0.046-0.0431.8639-0.42221.4953184.0574121.5028-1.9901
216.787-5.2517-4.38175.41891.82924.7752-0.0652-0.61320.76780.10870.5234-0.6708-0.12010.3122-0.44451.2246-0.29530.2271.3696-0.61331.4733162.1021129.05414.9419
224.9272-6.37882.10958.5015-2.33743.2618-0.8181-0.40672.54210.78030.6079-2.0928-1.48530.95220.2191.3406-0.38280.04641.2465-0.30321.5097167.9193132.7775.9165
233.76085.6323-2.90638.6918-3.33856.89011.0616-0.62452.5230.9337-0.22931.982-1.0727-0.2876-0.85261.05640.08450.22211.1178-0.22141.4772145.4167129.03670.668
244.7551-4.7048-4.79434.69134.76714.8577-1.30723.1555-4.4128-0.85150.363-0.74231.7492-0.41750.92491.09560.04690.15361.1042-0.16031.4851152.6339119.7528-10.6856
253.7281.6769-2.80998.8754-2.8957.4321-0.73240.2611-0.74620.5761-0.13820.1663-0.1331-0.91850.92040.94650.14480.06410.8988-0.28461.2657145.6996116.62121.0873
264.0895-3.0339-2.463.43534.34527.0426-0.284-0.4629-0.07690.85940.2348-0.14140.33650.52470.02980.9577-0.07820.11661.1169-0.10380.9988153.3967120.4199-0.1598
274.2319-4.90894.17119.1868-4.69054.1233-0.7904-1.01590.67111.4453-0.23781.3545-1.6142-1.4320.98281.45910.16830.36251.1999-0.28461.4311136.7648133.8458-9.0717
285.99581.3571-1.99652.82640.72076.2088-0.0430.6183-0.0456-1.1204-0.1529-0.05840.26690.20430.1631.78990.28230.00782.22340.06730.9468174.2553114.8028-93.5408
295.89891.49073.44563.46660.98176.62030.06611.2262-0.0164-0.5923-0.081-0.00950.07240.15020.02671.53760.23210.2571.91650.11411.1605175.1126115.6145-87.0302
307.70554.19755.64722.6214.17059.8026-0.6949-0.1871.388-1.0821-0.2592.0175-1.3578-1.02350.92791.38970.0546-0.34241.92040.48431.9448166.0446131.3165-73.4817
314.25432.14174.84737.93933.83976.0159-0.62470.18034.53490.7434-0.95062.9611-1.0359-0.55761.35331.2597-0.0249-0.14991.4365-0.49813.1217217.3387143.1336-22.0522
320.0240.0455-0.02480.0866-0.04880.07030.12270.47591.79820.21380.28621.4985-0.6313-0.5707-0.44111.7844-0.22420.58261.46810.57274.2006239.3181153.3205-23.1834
332.5808-2.28264.09524.1952-1.22999.1898-0.2820.73580.78330.08120.0923-1.0281-0.82311.45460.23131.2439-0.17970.48741.6365-0.29723.3119245.2731144.0788-21.3302
340.87181.5815-0.91954.5612-1.92135.9371-0.93492.01340.3293-0.89180.7276-1.6099-0.57360.00330.26662.1551-0.646-0.16472.47210.43812.7818254.3013148.486-35.0562
354.813.54092.23894.39831.63676.3433-0.30581.16980.516-0.8622-0.4829-0.8644-0.16990.53070.75021.53310.30240.25663.02270.91622.3937233.653138.1534-36.6422
369.904-0.09255.72340.30181.31869.6340.1741-0.07620.3965-0.0111-0.1281.03941.33040.2837-0.20061.96120.17260.06452.320.21632.181220.127125.9426-38.3051
373.46890.7661-0.33541.87261.27691.15940.50930.59510.72380.3296-0.3314-0.8682-0.3604-0.2249-0.20571.3454-0.34060.11131.62660.47862.7116235.4187136.7998-29.8408
382.9101-2.4315-1.31522.25320.90434.4737-0.22611.47930.2295-0.73930.5419-0.83420.09551.4318-0.25441.3334-0.11610.83862.30490.36352.591251.106135.6215-29.5579
394.2268-0.28165.44473.50840.13147.0891-0.19051.2968-0.5979-0.785-0.0658-1.07680.40460.81740.22641.83880.36850.5262.46290.40722.051238.6231130.008-39.7077
403.10782.05153.27587.36330.1514.18570.007-0.88910.75640.87960.4981.4045-0.0584-0.6931-0.49892.27440.11120.40772.81180.24562.0973220.1906126.5223-44.8398
418.26784.94012.05979.3569-2.04565.08890.3425-0.5214-0.0377-0.99620.6119-0.3977-0.29841.1692-0.87890.9040.08880.29291.0087-0.11410.9862140.3975122.7713-30.6455
423.37723.60965.46476.84936.4829.00510.287-0.29010.8447-0.63560.0935-0.193-1.1242-0.3882-0.38771.01490.03450.33131.0503-0.01611.4023139.5261132.5093-31.7137
438.67846.62545.73548.83946.63855.153-0.1967-0.39530.92870.1423-0.80431.9854-0.1866-2.15210.96910.76970.13780.130.99540.2161.3139126.8474125.9149-27.5203
443.6217-2.081-1.29812.64423.4468.627-0.15910.24840.43630.0987-0.15051.2432-2.0707-0.71830.31121.44890.05860.06830.85780.15241.5812130.8027133.2366-29.9285
457.77285.40158.21087.46375.52598.7969-0.48121.16380.9834-1.06760.1148-0.8986-0.98190.80150.33090.96420.13010.18021.08120.27721.4611133.8074132.0798-38.7488
469.9873.75746.72875.13772.98184.57070.0716-0.74560.28921.04760.55080.4255-0.2662-0.2148-0.64261.13070.09420.31470.9438-0.11041.6462145.8555140.0868-16.7514
477.48875.86565.27814.87485.00136.35290.2999-0.2480.06370.143-0.2504-0.5335-0.22240.2551-0.03391.06080.07870.16120.98150.02031.2176143.6534129.3818-18.6005
482.2762.88340.02894.9121-2.88396.7706-0.27810.676-0.3267-0.4179-0.1357-0.49170.44340.48540.37530.8874-0.01230.08671.09940.02820.9707134.1392108.9484-24.5459
496.57970.24652.11975.1349-0.3927.4838-1.4497-1.6684-3.25371.24570.9036-0.3992.23561.6650.58041.05220.3080.27591.28130.20851.5631125.5919109.6713-12.6163
502.2225-1.1703-1.30455.69515.65435.8727-0.3969-1.5314-2.54051.0277-1.61551.29150.4944-0.89792.08731.1457-0.11470.26881.2508-0.01671.3768133.6344119.7481-8.6758
515.35631.264.16322.53532.215.2656-0.2202-0.1407-0.2740.01670.16990.53920.0047-0.0090.06570.92680.10420.22340.89980.16141.4481126.4233118.8478-19.1385
528.44024.6252-4.31096.3075-3.0889.71510.0543-0.37511.50251.1933-0.59160.4397-1.5447-0.92530.52741.03410.12180.22040.7985-0.05771.4458122.5884119.9497-15.6768
538.50976.7143-2.19316.5048-0.03362.96210.3796-1.2715-1.40830.9148-0.1618-0.59360.4237-0.3161-0.18280.96480.1240.01520.95980.24590.9527131.3864117.2429-19.0348
546.09745.10891.62124.29261.34170.44640.0726-0.05521.09120.21010.1722-1.2879-0.55080.8665-0.23621.6589-0.21440.05991.9767-1.0974.088238.8464166.7612-1.7097
554.78923.07083.49685.58012.4663.35360.14220.0535-0.47210.3043-0.0874-0.8183-0.16390.6232-0.09021.6781-0.6896-0.16331.9874-0.94943.3972249.2377161.8732-0.9229
560.1432-0.2191-0.14030.5102-0.28841.7701-1.11050.4450.7065-0.35480.01380.0677-0.55880.59580.94241.3212-0.56630.00561.9967-0.46094.5323244.5428159.1695-10.8675
574.4872-1.38572.83431.23180.74685.11640.23960.62931.46310.9154-0.08450.3202-0.99460.9371-0.17951.5893-0.4763-0.07271.4925-0.71764.6459239.1926165.0359-6.0069
580.68271.35371.88874.54745.45447.0878-0.5277-0.40582.2777-0.15550.16170.1174-2.14940.76580.36642.0981-0.0773-0.2241.6597-0.49234.1402229.1974172.7127-14.0111
590.5159-1.28370.86165.5808-1.68361.6950.3295-0.46841.39370.4265-1.2143-0.9162-0.48160.04510.8551.2217-0.24720.21212.2045-0.84032.767225.9039147.2579-4.8184
607.1207-4.1681-1.01514.0319-2.74427.14920.101-0.47230.8298-0.59520.4981.96930.833-0.4288-0.61.0634-0.26360.0232.2063-0.79641.9502223.1257124.7294-6.512
610.77710.5397-0.73861.92090.04170.89220.14960.46130.0850.6313-0.26880.4544-0.575-1.10550.03421.85760.27210.02753.4723-1.97213.8997221.2187160.124129.1808
621.15820.5279-2.850.5749-0.87177.53350.1675-0.44190.98430.73170.7097-1.4658-2.35790.2524-0.88862.4720.3472-0.17783.1519-2.25784.0208227.1676164.123225.4877
635.99481.3019-1.02680.2835-0.19061.6897-0.4705-0.41310.01210.1479-0.45120.80410.3238-0.4660.92381.42190.1634-0.063.5771-1.37562.5883225.1728140.388918.44
643.921-0.2577-0.67976.3476-3.15061.73270.275-1.00411.21071.25060.3817-0.46610.1268-0.2764-0.57881.4265-0.05770.08753.2765-1.22932.0482218.3803133.942214.2005
650.253-0.73330.4542.1223-1.31190.8110.9495-2.29421.42465.251-0.7411-1.1942-2.98661.41-0.19983.5748-0.125-0.33163.3721-2.23274.3765230.6553167.716132.2988
662.8087-3.0151-0.46544.98852.64254.3130.27310.12730.4397-0.43660.1806-1.0577-0.35430.5689-0.57692.99971.09391.09732.5842-1.0833.3096223.1231170.509540.3318
670.1842-0.1409-0.08760.44280.30350.20710.5572-0.99690.96720.3637-0.93842.1742-1.3216-1.24370.4032.18010.23420.29273.7551-1.43153.2006214.9353157.637237.1287
680.7022-1.9869-1.37345.64023.91162.7428-0.11821.2014-1.1154-1.1027-0.6071.24170.8243-0.54840.65062.1680.0151-0.22262.7434-0.96682.799226.1607154.103535.6728
699.1241-1.7288.58037.7177-4.10799.14340.22610.8770.6824-0.56430.418-0.0495-1.0257-0.6461-0.54921.1509-0.01760.23231.0828-0.06121.6107213.3945118.5986-69.4209
707.3022-1.10845.84622.349-1.03394.72730.14640.37620.45730.1271-0.0602-0.1484-0.39781.0593-0.10431.15460.05690.2711.5820.01961.5581217.5239114.8955-62.7891
715.07191.2609-5.85147.1135-1.45939.77910.8044-0.56431.0490.0107-0.3145-1.4447-0.36391.5702-0.50441.149-0.02620.08791.60480.08651.8199221.5646121.9852-64.6673
726.86276.1054-1.67099.3644-4.82539.8984-0.19750.57771.5746-0.24970.04930.0448-0.4215-0.64460.14441.13470.11560.03681.56630.03831.6455211.6204125.9002-64.8888
735.155-2.03784.08857.39981.61544.8186-1.16041.43411.1161-0.4462-0.4173-2.7075-2.061.63521.68781.5483-0.22340.17911.63580.44881.8836211.2455129.9352-69.847
741.7277-1.86222.13575.5981-2.69992.7610.40970.7764-0.2384-0.2607-0.685-0.19880.11780.61110.15251.273-0.00210.39681.5491-0.25151.3513193.8593110.2807-57.6469
754.9144-5.06096.37825.3611-7.14819.50740.7640.4675-0.4574-0.4601-0.24420.37111.36271.343-0.38431.10620.1635-0.13961.1657-0.01341.2611153.291489.0537-13.6889
764.38990.4813-1.92463.77571.35781.57840.00120.0423-0.09130.54440.0308-0.39610.60120.57170.01241.43370.3322-0.31041.54530.04041.5339173.540278.979711.0704
773.7907-5.89790.15879.36-0.9552.6765-0.6608-0.953-0.2447-0.52670.25160.66561.65-0.3020.46471.45750.16510.12671.8308-0.38652.2484274.5215116.4646-8.05
784.161-4.29673.55034.9746-3.34353.3758-0.0284-0.31051.0287-0.02510.05930.1921-0.2855-0.1865-0.05261.150.2706-0.08591.747-0.05682.1549269.1567120.7419-4.6984
792.72964.1176-0.11058.3488-3.92167.22440.389-1.05981.12360.0342-1.2372-0.1045-0.40680.35580.81941.13530.04420.04562.1222-0.5762.2916276.2849122.3108-0.5839
805.284-0.2648-3.27352.5236-3.90478.6312-0.2188-2.6126-0.8280.98140.4491-1.0782-0.33680.8623-0.37031.4420.0199-0.24142.32280.05611.6308265.748104.26688.9157
818.81813.71581.65093.51161.88021.20280.1097-1.0590.08180.40210.18911.54820.7198-1.6045-0.28381.6106-0.2914-0.04933.01020.54852.0893250.102998.030913.1762
820.5756-1.144-1.72456.84340.45017.5837-0.2691-1.1292-0.59630.10810.0760.7176-0.0115-0.01130.26731.1058-0.0411-0.10662.22850.09482.1885241.2191103.02421.8585
838.68874.7448-8.26953.2951-5.47249.16620.2023-0.76180.0350.2659-0.50130.2869-0.5858-0.40310.29942.56690.8426-0.43773.1584-0.181.5517219.8828114.976434.0476
847.57141.2621-0.33074.13410.0630.01710.0137-0.7837-0.820.81770.38022.3248-0.0641-1.5635-0.39781.27480.1063-0.11835.0163-0.2032.2321232.4743116.508138.3713
850.30111.14620.14294.3620.54270.0839-0.16090.3642-0.8553-0.1525-0.7670.00840.1539-0.1910.84891.5509-0.09550.30453.8376-0.28682.2299228.5528119.064530.5144
863.0407-2.30933.77572.5309-1.62336.6965-0.2257-1.60911.6599-0.16951.09-2.80630.73791.8413-0.80251.96630.3560.7693.2304-0.70952.5137215.5061122.115426.9344
874.57980.03910.18610.856-0.24822.7337-0.7394-1.72911.0670.274-0.12730.12970.3324-1.08560.80011.36940.0969-0.14143.4864-0.98791.6608216.698132.462120.879
884.12035.6869-4.30919.8512-6.03564.5232-0.44163.86371.0006-2.59390.80710.1506-0.6043-0.8008-0.36041.73470.1920.09651.9890.14791.0718142.0094111.0049-74.1215
899.2478-5.0830.92736.43860.00178.23770.87680.9921-0.4804-1.2652-0.08030.3206-0.3867-0.4128-0.77161.1975-0.0506-0.10631.19610.0420.9858145.2786104.6005-66.6048
909.2755-0.67240.42823.8269-0.46533.42990.244-2.0012-0.31110.27770.01880.16310.23190.4348-0.27850.96530.0562-0.1321.5319-0.00071.1536143.9078102.0291-56.3321
915.6897-1.1566-5.7067.07781.99875.8237-0.80671.057-1.0494-0.4404-0.02141.74431.7043-2.36140.87361.358-0.2806-0.18161.57390.05441.6567131.300298.2801-63.649
922.6669-0.0960.37130.8326-0.81851.44470.1093-0.5220.0610.876-0.0210.26540.25010.2645-0.0741.68030.06980.47561.07380.06771.4861117.037676.877814.7634
932.73530.53740.99411.2546-1.62836.99790.094-0.18930.62730.4079-0.00160.85740.1506-0.013-0.07021.3874-0.06770.44160.93220.02611.7679114.643277.328510.1835
949.39676.82457.07998.99266.36785.7002-0.8621-0.60931.294-0.4331-0.07620.6601-1.7932-0.37440.87881.83890.03670.8230.9361-0.12532.0759108.891286.71319.8763
954.50254.9145-0.59255.4145-0.64866.4234-0.92720.20960.7047-0.91310.12481.1635-0.929-0.0210.6431.21030.00210.1641.08760.67253.1065100.468679.14534.764
966.28970.82161.01576.79654.93136.047-0.0695-1.0012-1.7440.4584-0.77760.88940.996-0.26660.89121.7858-0.17720.71550.94280.0822.0327100.620475.111415.6224
975.3768-2.2066-3.42125.84543.38913.00290.46650.62910.2837-0.1260.32960.14770.0997-0.4302-0.83651.0338-0.0542-0.01920.98230.25281.3988120.499280.8602-38.6835
986.05733.75043.42355.51033.49893.4343-0.1190.09080.0806-0.55310.15360.6105-0.0993-0.18970.01480.9766-0.0783-0.0131.03540.23641.3491122.477784.6883-35.8439
996.2435-3.96382.95528.6649-2.72458.2153-0.03860.6642-0.21040.05580.61150.10870.45190.729-0.59171.435-0.1103-0.03491.5155-0.06121.4366138.547685.7873-44.4903
1004.2214-4.501-2.41445.5260.86065.4296-0.4562-0.7582.17460.17310.4977-1.3935-2.90120.5882-0.05271.6754-0.16740.68441.1636-0.44222.6409180.733140.0977-63.7199
1016.17235.92585.96088.35567.08478.2517-0.85630.42551.7372-1.28190.05880.3864-1.99870.24140.78492.7709-0.06770.53361.40150.16292.1346175.0168141.192-71.645
1026.0277-1.4354-3.93141.67081.92888.1693-0.8071-0.2386-0.1659-0.5601-0.8137-0.55560.0280.5071.49181.53930.34980.16142.02770.44091.6204172.8734128.9904-76.8695
1032.90013.18942.94534.91176.24369.61050.03062.01211.1329-2.251-0.0564-1.7355-1.88542.0512-0.0131.4340.2290.56971.41720.38971.7634181.744132.9492-74.7656
1044.384-3.9643-4.26523.69263.86464.1612-0.11960.50820.3161-0.40150.6104-2.6011-0.73871.9253-0.44961.31360.02820.07991.82580.0171.4525187.1095128.3875-66.1218
1055.7365-2.2281-2.1695.36854.19627.38850.6401-0.11090.48070.10480.24240.0959-0.2862-0.1904-0.82791.29330.13490.27811.41720.23690.9697176.2516126.9071-67.1188
1068.0582.7137.55992.23383.62868.0648-0.46360.18680.11780.10160.1064-0.3112-0.10570.62060.31641.56460.17860.29341.60170.18471.5583193.2912125.7743-71.0514
1070.67280.526-2.26833.8155-2.53197.7636-0.30410.6601-0.8192-1.33371.05761.59170.9927-3.4953-0.86352.09480.5436-1.11063.2014-0.76712.719252.2977111.794627.9315
1082.4129-0.7183-0.36260.21510.09970.1877-2.0693-3.04710.97843.91751.1466-1.69510.13930.60690.86672.73940.6546-0.5793.91020.22882.1009252.096897.936241.6223
1092.07381.8681-2.57552.072-1.0147.5858-0.5122-0.1595-0.7590.51671.01841.06680.2277-0.9436-0.48071.56430.3169-0.02923.60080.51512.3002247.560491.101136.3682
1102.4491-0.5707-0.28310.26350.21160.1938-1.1007-3.23030.53060.72840.4977-0.2065-0.2511-0.36660.51291.3814-0.2551-0.84824.14180.4353.1809247.4566103.067228.6129
1110.73982.38960.28787.8711.835.0346-0.08030.98710.71960.13350.3273-0.04550.01930.3162-0.22651.60240.201-0.02383.95420.55022.3206250.741294.349727.9506
1127.719-2.34493.96994.0918-4.99326.56070.5442-0.494-1.33260.7886-0.2758-1.77491.14262.7049-0.30241.60390.4112-0.12383.03360.45782.1418242.436194.837616.8462
1132.0691-1.54463.0941.8724-1.7077.43910.4442-0.2363-0.08930.06130.10.58641.0322-0.5126-0.63991.4741-0.16320.14450.90820.20911.6061108.299641.7275-20.3474
1148.4988-2.21183.35085.9015-2.83698.56390.2842-0.7010.4611.41920.10871.3282-0.3173-0.7721-0.31231.4382-0.03640.11531.3330.19861.4472105.873251.5743-15.3762
1153.9294.3685.08637.54757.17497.4471-0.27041.17761.4077-0.49310.2704-0.0667-1.85491.18630.03591.318-0.24430.00011.24330.58252.0676103.842752.1834-32.0001
1164.0836-1.59520.80574.55873.75714.36980.0596-0.2366-0.1476-0.295-1.47911.16621.0815-0.82141.35952.0695-0.2753-0.04081.86480.02961.7393.412447.525-40.302
1175.0937-5.6014-0.54316.4810.63640.06050.58040.2148-1.1131-0.1631-0.38651.54390.7255-0.3575-0.21871.6524-0.5556-0.27042.0178-0.53472.4498251.7956124.4143.07
1182.6337-1.73372.76241.2081-1.85352.91970.2164-0.63441.1023-0.6017-0.47470.5379-0.3012-0.28320.26551.82190.0698-0.22311.5086-0.7782.124248.4551129.28394.9686
1194.62240.34310.97481.56340.2323.2642-0.6345-0.21690.56760.1062-0.24480.1086-0.6421-0.08640.7591.6959-0.74150.28983.2841-1.43112.588254.3587132.455311.409
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 1401:1532)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)A0
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)B7 - 25
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)B26 - 64
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)B65 - 86
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)B87 - 122
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)B123 - 148
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)B149 - 226
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)B227 - 240
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)C2 - 112
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)C113 - 207
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)D2 - 34
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)D35 - 67
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)D68 - 148
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)D149 - 181
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)D182 - 209
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)E5 - 14
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)E15 - 27
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)E28 - 50
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)E51 - 63
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)E64 - 79
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)E80 - 86
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)E87 - 103
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)E104 - 140
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)E141 - 154
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)F1 - 32
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)F33 - 92
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)F93 - 101
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)G2 - 11
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)G12 - 20
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)G21 - 52
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)G53 - 57
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)G58 - 79
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)G80 - 92
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)G93 - 109
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)G110 - 129
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)G130 - 144
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)G145 - 156
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)H1 - 18
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)H19 - 29
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)H30 - 41
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)H42 - 53
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)H54 - 62
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)H63 - 72
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)H73 - 85
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)H86 - 95
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)H96 - 100
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)H101 - 106
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)H107 - 116
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)H117 - 127
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)H128 - 138
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)I2 - 25
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)I26 - 32
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)I33 - 53
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)I54 - 88
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)I89 - 97
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)I98 - 117
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)I118 - 128
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)J3 - 29
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)J30 - 42
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)J43 - 47
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)J48 - 70
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)J71 - 78
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)J79 - 85
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)J86 - 93
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)J94 - 100
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)K11 - 34
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)K35 - 57
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)K58 - 75
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)K76 - 100
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)K101 - 110
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)K111 - 126
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)L5 - 32
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)L33 - 128
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)M2 - 14
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)M15 - 21
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)M22 - 61
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)M62 - 83
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)M84 - 93
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)M94 - 119
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)N2 - 11
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)N12 - 16
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)N17 - 24
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)N25 - 29
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)N30 - 61
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)O2 - 15
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)O16 - 49
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)O50 - 73
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)O74 - 88
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)P1 - 19
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)P20 - 43
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)P44 - 52
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)P53 - 62
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)P63 - 83
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)Q2 - 17
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)Q18 - 82
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)Q83 - 100
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)R19 - 23
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)R24 - 28
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)R29 - 36
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)R37 - 43
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)R44 - 52
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)R53 - 76
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)R77 - 88
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)S2 - 12
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)S13 - 25
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)S26 - 35
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)S36 - 40
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)S41 - 70
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)S71 - 81
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)T8 - 66
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)T67 - 75
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)T76 - 91
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)T92 - 106
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)U2 - 8
118X-RAY DIFFRACTION118chain 'U' and (resseq 9:15)U9 - 15
119X-RAY DIFFRACTION119chain 'U' and (resseq 16:25)U16 - 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