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- PDB-6cap: Crystal Structure of 30S ribosomal subunit from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 6cap
TitleCrystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin
Components
  • (30S ribosomal protein ...) x 19
  • 16S Ribosomal RNA rRNA
  • RIBOSOMAL PROTEIN S5
  • RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
  • RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
KeywordsRIBOSOME / translation / miscoding / antibiotic / sisomicin
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
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 S7 / Ribosomal protein S7/S5 ...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 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 / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; 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 / 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 / Few Secondary Structures / Irregular / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / 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 / Ribosomal protein S2, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18
Similarity search - Domain/homology
Chem-SIS / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 ...Chem-SIS / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS5 / 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 / 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)
Thermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsDeMirci, H.
CitationJournal: To Be Published
Title: Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin
Authors: DeMirci, H.
History
DepositionJan 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns_shell ...pdbx_struct_conn_angle / reflns_shell / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S Ribosomal RNA rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: RIBOSOMAL PROTEIN S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein Thx
Y: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
W: RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)779,099278
Polymers772,39623
Non-polymers6,703255
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)400.970, 400.970, 175.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 3 types, 3 molecules AYW

#1: RNA chain 16S Ribosomal RNA rRNA


Mass: 494168.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: GenBank: 55771382
#22: RNA chain RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria)
#23: RNA chain RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')


Mass: 4815.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria)

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30S ribosomal protein ... , 19 types, 19 molecules BCDFGHIJKLMNOPQRSTU

#2: Protein 30S ribosomal protein S2 /


Mass: 26987.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3 /


Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4 /


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#6: Protein 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7 /


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#8: Protein 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY9
#9: Protein 30S ribosomal protein S9 /


Mass: 14279.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#10: Protein 30S ribosomal protein S10 /


Mass: 11299.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11 /


Mass: 12319.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12 /


Mass: 13850.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: Protein 30S ribosomal protein S13 /


Mass: 13365.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY6
#15: Protein 30S ribosomal protein S15 /


Mass: 10390.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16 /


Mass: 9924.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17 /


Mass: 11721.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY7
#18: Protein 30S ribosomal protein S18 /


Mass: 8155.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19 /


Mass: 9203.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20 /


Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 2960.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

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Protein , 1 types, 1 molecules E

#5: Protein RIBOSOMAL PROTEIN S5 /


Mass: 16331.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P62665, UniProt: Q5SHQ5*PLUS

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Non-polymers , 4 types, 477 molecules

#24: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 252 / Source method: obtained synthetically / Formula: Mg
#25: Chemical ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin / Sisomicin


Mass: 447.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H37N5O7 / Comment: antibiotic*YM
#26: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.59 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5 / Details: 17% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.12→39.908 Å / Num. obs: 244903 / % possible obs: 97.7 % / Redundancy: 97.904 % / Biso Wilson estimate: 127.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 1.011 / Rrim(I) all: 1.017 / Χ2: 0.769 / Net I/σ(I): 7.64 / Num. measured all: 23977077 / Scaling rejects: 6117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. possibleNum. unique obs% possible allCC1/2Rmerge(I) obsRrim(I) all
3.12-3.243.2180.19561839183441300070.9
3.2-3.2978.8140.441410147179671789299.6
3.29-3.3897.1550.59168671417367173611000.145
3.38-3.4998.6590.74167226316958169501000.202
3.49-3.699.1360.89162395316387163811000.39.069.105
3.6-3.7398.6761.17157229815937159341000.4227.1947.231
3.73-3.8793.4131.441428381153101529199.90.5575.7585.789
3.87-4.03105.1522.19155530114794147911000.7323.9683.987
4.03-4.21107.3862.99152412414198141931000.822.9522.965
4.21-4.41107.1333.98145593413594135901000.8912.2362.247
4.41-4.65104.9765.25135544412912129121000.9371.7081.716
4.65-4.93101.8066.61124926612275122711000.951.3561.363
4.93-5.27111.5999.16128852511548115461000.9781.0191.023
5.27-5.7110.39111.6118726010757107551000.9860.7930.796
5.7-6.24105.38213.721047915994599441000.990.6510.654
6.24-6.98107.818.529721379026901899.90.9940.4560.458
6.98-8.06109.87729.14879122800180011000.9980.2720.273
8.06-9.8799.79236.756788866824680399.70.9990.1880.189
9.87-13.95105.28157.425636755355535410010.1040.104
13.95-39.90890.49861.582638933114291693.610.0650.066

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementResolution: 3.4→39.908 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.91
RfactorNum. reflection% reflection
Rfree0.2298 1580 0.82 %
Rwork0.1829 --
obs0.1833 193729 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 395.79 Å2 / Biso mean: 142.3971 Å2 / Biso min: 57.36 Å2
Refinement stepCycle: final / Resolution: 3.4→39.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19088 32943 507 0 52538
Biso mean--138.39 --
Num. residues----3910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456678
X-RAY DIFFRACTIONf_angle_d0.82384131
X-RAY DIFFRACTIONf_chiral_restr0.04310527
X-RAY DIFFRACTIONf_plane_restr0.0054910
X-RAY DIFFRACTIONf_dihedral_angle_d16.93730812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.50970.4011430.35271731317456100
3.5097-3.6350.33131410.32581730017441100
3.635-3.78050.34671430.29171734417487100
3.7805-3.95240.2861420.2641730317445100
3.9524-4.16060.2941440.2241740117545100
4.1606-4.42090.25181430.19011738717530100
4.4209-4.76180.21221430.17311744917592100
4.7618-5.240.19481440.15231747117615100
5.24-5.9960.18981450.14131758117726100
5.996-7.5460.22641460.151767517821100
7.546-39.91070.18081460.148179251807199
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)
10.40110.1316-0.1510.4437-0.07370.32410.02580.0387-0.01640.16830.08280.14110.0837-0.0125-0.10550.94230.10130.09090.8346-0.0431.2755143.858783.602-12.7601
21.0617-0.16150.1640.4943-0.1180.32610.0897-0.58280.41470.24980.0069-0.112-0.22010.1178-0.09010.974-0.22280.14451.3922-0.51911.3214222.4408129.61569.0598
31.79520.6558-0.61340.2612-0.34070.2227-0.2251-0.0117-0.5124-0.1470.243-0.40960.16250.0747-0.01371.10340.11970.00851.1159-0.08261.4668164.771370.142-26.3445
49.244-6.70956.85844.8853-4.97815.0884-0.3159-2.70860.11621.84743.07312.3229-1.6135-0.9384-2.76682.29240.56640.45223.52160.49292.2761203.6749111.9569-33.6588
51.9693-3.2679-1.85079.28255.90155.79960.3637-0.183-0.1472-2.89070.5894-0.4213-1.40250.4196-0.93841.4768-0.1060.03860.7830.1461.5752155.4271158.0335-34.9841
66.3061-1.6316-1.41925.20875.84028.85830.75470.24720.9231-0.5875-0.5261.1494-0.6934-1.2417-0.18161.27660.04750.34050.68150.14912.0746149.55156.247-27.8866
73.8605-2.9348-3.81395.30522.47754.61960.2619-0.1231.8024-0.56720.1239-0.9804-1.92841.4168-0.48631.3252-0.12440.35271.1023-0.09161.7758166.4101162.9289-19.4978
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936.322.17074.73365.47764.55517.5605-0.01760.09641.5717-0.09140.25510.134-0.77760.5132-0.26780.9613-0.10810.31630.7181-0.04651.6234115.626177.425410.6372
945.61572.98214.18429.50426.5756.462-0.38940.02223.1989-0.58110.09780.6674-4.44450.14410.23951.818-0.00750.81020.83560.08811.8794110.290886.652920.6611
956.03646.31921.69976.61431.79245.8758-0.65520.12660.6863-1.43110.22641.6855-2.4767-0.52650.40371.46640.37620.2781.11030.88992.1026101.315879.47325.8551
969.2691-5.812-2.1449.26174.6852.4858-0.5836-1.1754-2.93792.4707-0.30811.97010.0651-0.12881.00221.5863-0.15680.58621.05630.26771.659101.814775.146416.6655
979.93398.47070.68578.2641-1.92256.5188-0.21490.79210.0019-1.10860.3010.2065-0.5388-0.1601-0.05630.59010.0498-0.11160.61310.15841.1446120.06781.0126-38.4681
980.4072-0.8766-0.09952.09810.1172.44590.0196-0.0887-0.1015-0.22810.15580.67710.3745-0.1882-0.17990.7495-0.11780.06770.91950.15041.3118122.081884.8724-35.7
994.2853-5.67414.88537.961-5.40018.24040.22951.4930.4348-0.5917-0.0808-0.7463-0.60771.4795-0.1611.0257-0.23310.11461.2203-0.16511.166138.14485.8894-44.8932
1007.24221.6156.14931.60941.68635.3673-1.1674-3.85467.96080.13260.0120.6635-3.4716-1.54531.14711.55580.31460.30651.5031-0.28832.5653180.333140.2588-64.1952
1017.25496.07777.11675.78696.21977.0778-2.1193-2.53818.18230.6350.01371.3131-5.2103-2.17522.07622.6270.34470.96391.6785-0.09933.2173175.1464141.8437-72.0721
1023.3866-5.1217-2.73728.78281.90137.0711-0.1335-0.1499-0.3805-0.1553-0.7151-1.4382-0.15310.50890.86071.04360.07710.05241.61650.17851.9468172.5125129.2946-77.3066
1036.97441.81456.30222.34314.429.82260.641.50432.871-2.4201-1.1112-2.2427-3.5853-0.70360.42421.1960.53050.50750.75160.44311.9535181.4795133.3577-75.1493
1046.0579-5.8011-4.59025.56234.47144.19521.215-0.45182.06020.09340.6776-4.6131-0.68484.5158-1.85560.81640.0510.0751.7541-0.53261.624186.6216128.8092-66.6676
1054.7224-5.2524-3.05919.56647.16325.7710.7378-0.49140.3016-0.28920.0181-0.547-0.4529-0.7305-0.75021.024-0.01090.14961.12960.27990.9894175.8442127.2688-67.6324
1069.39281.17973.90090.5289-0.19513.0002-0.0675-0.3107-0.30.2620.1061-0.31780.05360.4002-0.03781.35020.24590.04531.4162-0.01811.6275193.0878126.1664-71.2843
1070.21821.1553-1.07086.0034-5.39556.373-0.8513.6611-1.0241-2.15760.67721.38133.4008-3.84460.16711.3948-0.2794-0.1832.2328-0.45731.3415251.8598113.069827.8657
1085.6593-5.8724.1356.2146-4.46083.2565-3.2144-4.3682.55275.94151.6827-1.6769-2.64260.79631.4022.08960.1014-0.3732.1777-0.40921.4431250.8109100.073542.2716
1091.9781-3.02333.15144.6832-4.76915.0273-0.44-0.0826-0.49260.89180.1797-0.9205-0.0552-1.28760.19720.959-0.3737-0.49442.8402-0.12082.1315246.264693.498636.8353
1102.00064.91356.98512.20443.25334.8551-1.3066-5.77672.74360.7129-0.7765-0.0649-2.7169-1.131.9591.7911-0.4702-0.4132.42020.19751.3479246.5382105.089128.706
1113.34381.19294.24418.62070.85375.4473-0.5086-1.5698-0.6809-0.28110.5704-0.764-0.58490.6973-0.1341.39590.03010.04772.09420.00251.3551249.522596.314928.808
1123.76891.30113.96757.21262.03364.7635-0.69183.0804-2.1012-1.08450.5635-1.0780.05482.15180.06971.14270.03430.34331.8869-0.25271.162241.076497.050517.8976
1133.3293-2.28763.95251.7009-2.7574.52150.3726-0.0388-0.4460.13350.29480.61470.0566-0.2253-0.71090.996-0.09740.27050.75480.21251.5287108.079742.1021-20.1431
1145.69016.2771-5.54126.9264-6.11215.40911.50430.76771.24391.30581.08912.69750.37110.894-2.53030.97260.0389-0.06621.18970.10071.0975105.770952.0239-14.8062
1159.23715.856.09395.62775.43875.7064-0.50971.24961.2464-0.8944-0.1975-0.6299-2.1082.91940.58431.046-0.19010.30111.35420.58012.0764103.319552.4457-31.6119
1165.0509-3.68331.81854.70980.84433.4570.6749-0.7844-1.286-0.5416-2.61072.71970.6207-2.24721.81641.0814-0.2112-0.07931.5290.04491.510692.72648.1442-39.6516
1175.7488-5.29724.54356.6486-2.09916.08550.68760.2014-1.62470.3592-0.26212.80810.23840.3039-0.41230.9173-0.05980.04771.3448-0.51341.9887251.2144124.5171.8791
1183.77-1.28753.52742.3212-0.53923.5503-0.8778-0.42373.1302-0.37460.32641.4018-1.066-0.02980.48121.30820.1112-0.26610.8365-0.23511.913248.0744129.60423.7792
1195.9924-1.06352.05415.82840.88837.0309-0.4234-2.57841.24723.1608-0.68-1.48-0.79840.01490.9811.888-0.6194-0.30712.2404-0.51811.3541253.9407132.92649.8847
1206.32085.4644-5.52975.0438-4.85464.86290.0414-0.27532.45840.65711.01840.6377-0.7308-0.171-0.99431.54050.231-0.64821.994-0.62442.5498191.848103.7975-1.0347
1219.2836-1.11074.73025.56921.0032.88490.31650.17620.91631.4626-0.6613-0.42131.24641.47430.34751.4450.1863-0.0562.2182-0.50721.6547205.996193.00826.4465
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)A1401 - 1532
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)A1533 - 1541
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
120X-RAY DIFFRACTION120chain 'Y' and (resseq 1:6)Y1 - 6
121X-RAY DIFFRACTION121chain 'W' and (resseq 28:42)W28 - 42

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