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- PDB-5wnv: Crystal Structure of 30S ribosomal subunit from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5wnv
TitleCrystal Structure of 30S ribosomal subunit from Thermus thermophilus
Components
  • (30S ribosomal protein ...) x 20
  • (RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)- ...) x 2
  • 16S Ribosomal RNA rRNA
KeywordsRIBOSOME / smFRET / mRNA methylation / translation / decoding
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 / 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 S2, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / 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-B6M / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...Chem-B6M / : / : / 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 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsDeMirci, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51266 and GM099687 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.
Authors: Choi, J. / Indrisiunaite, G. / DeMirci, H. / Ieong, K.W. / Wang, J. / Petrov, A. / Prabhakar, A. / Rechavi, G. / Dominissini, D. / He, C. / Ehrenberg, M. / Puglisi, J.D.
History
DepositionAug 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 21, 2018Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 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.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.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.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_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: 30S 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
a: RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)-3')
b: RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)781,938299
Polymers774,23123
Non-polymers7,707276
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)400.000, 400.000, 173.000
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 , 1 types, 1 molecules A

#1: RNA chain 16S Ribosomal RNA rRNA


Mass: 494170.781 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

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30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S ribosomal protein S2 /


Mass: 27217.490 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: 22975.588 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
#5: Protein 30S ribosomal protein S5 /


Mass: 16460.193 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: Q5SHQ5
#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: 11398.308 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: 12606.369 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: 13921.479 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: 10447.213 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: 9995.546 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: 11722.904 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: 8497.198 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: 9260.796 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: 3089.655 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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RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)- ... , 2 types, 2 molecules ab

#22: RNA chain RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)-3')


Mass: 1875.185 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
#23: RNA chain RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)-3')


Mass: 4979.135 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Non-polymers , 5 types, 503 molecules

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


Mass: 24.305 Da / Num. of mol.: 251 / Source method: obtained synthetically / Formula: Mg
#25: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: K
#26: Chemical ChemComp-B6M / (1R,2S,3S,4R,6R)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-alpha-L-altropyranosyl)-beta-L-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-allopyranoside


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14
#27: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 227 / 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: 4.47 Å3/Da / Density % sol: 72.48 %
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: 2.92→39.801 Å / Num. obs: 296028 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 106.516 % / Biso Wilson estimate: 118.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.57 / Rrim(I) all: 0.573 / Χ2: 0.986 / Net I/σ(I): 14.44 / Num. measured all: 31531631 / Scaling rejects: 14251
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured obsNum. possibleNum. unique obs% possible allMean I/σ(I) obsCC1/2Rmerge(I) obsRrim(I) all
2.92-2.9970.2081242955220971770480.1
2.99-3.07100.0921330172153321311990.21
3.07-3.16114.0112381794209202089199.90.580.289
3.16-3.26113.2162305421203772036399.90.960.4778.4528.49
3.26-3.37111.9192204689197161969999.91.320.5936.3476.375
3.37-3.49109.5332089456190911907699.91.770.6864.7894.811
3.49-3.62102.7111891006184401841199.82.390.7713.6293.647
3.62-3.77114.026202875417796177921003.840.8942.3572.368
3.77-3.93112.824192218617039170371005.610.941.7231.731
3.93-4.13110.95181070616321163201007.820.9691.2991.305
4.13-4.35106.9581662659155471554510010.760.9830.9710.976
4.35-4.61105.6611550993147061467999.814.710.990.6970.7
4.61-4.93112.8131567535138961389510020.040.9960.5230.525
4.93-5.33111.521442286129341293310025.10.9970.4020.404
5.33-5.83104.8391244015119091186699.630.280.9980.3140.316
5.83-6.52110.9521202276108401083610036.190.9990.2570.258
6.52-7.53110.22210615489631963110051.350.9990.1670.168
7.53-9.22100.0418114368169811199.367.1310.110.111
9.22-13.05103.1776615736413641210099.3510.0640.064
13.05-39.80190.2523173263726351694.4122.2410.0390.039

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 3.3→39.801 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 1407 0.68 %
Rwork0.179 206893 -
obs0.1791 208300 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 468.06 Å2 / Biso mean: 136.1624 Å2 / Biso min: 53.17 Å2
Refinement stepCycle: final / Resolution: 3.3→39.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19119 32959 564 0 52642
Biso mean--124.82 --
Num. residues----3925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256589
X-RAY DIFFRACTIONf_angle_d0.50283967
X-RAY DIFFRACTIONf_chiral_restr0.0310443
X-RAY DIFFRACTIONf_plane_restr0.0034914
X-RAY DIFFRACTIONf_dihedral_angle_d13.68430410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.41790.34381390.292046820607100
3.4179-3.55470.27431390.26692048220621100
3.5547-3.71630.27771400.22692050520645100
3.7163-3.91210.22821400.19332058920729100
3.9121-4.1570.22631400.1792056320703100
4.157-4.47750.20051400.16352062020760100
4.4775-4.92740.16911400.14862069520835100
4.9274-5.63870.19911410.14992076620907100
5.6387-7.09750.16131420.16672084520987100
7.0975-39.80440.19121460.1798213602150699
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)
10.46680.1914-0.21660.4793-0.10540.44330.0114-0.01170.02810.16490.09840.12930.11610.075-0.11350.71970.13650.0470.6987-0.03170.9942143.168983.03-12.8617
21.0944-0.24860.12330.4909-0.05570.43230.0251-0.79980.49980.3102-0.0069-0.1128-0.2080.0735-0.02810.9575-0.25790.09741.641-0.58081.3182221.0716128.88759.3731
31.75010.707-0.87520.3465-0.52190.3561-0.3095-0.0393-0.4469-0.18060.256-0.35190.20950.10390.05110.96920.1346-0.00160.956-0.05491.1798162.522369.0051-26.2198
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903.3771-3.4567-5.1398.15282.82549.06990.5105-2.2291-0.86620.34360.16050.22850.37850.7561-0.68290.7861-0.1054-0.21420.95320.07580.9436142.8197101.5955-57.0076
915.0133-1.6433-0.55377.03423.46025.40780.64480.6438-4.6074-0.1348-1.01311.0981.9695-2.07890.25840.9035-0.1449-0.47241.25930.06841.9841130.418897.5824-64.6233
924.17811.90965.69258.0870.02438.67950.4685-0.51740.5591.4389-0.17320.7728-0.55620.2189-0.31551.2390.00310.44650.8351-0.06681.2218117.567976.222315.1557
934.9567-1.210.50829.02265.31136.83710.17940.00891.3771-0.32950.4778-0.3064-0.52950.3674-0.70260.79250.01030.29920.6263-0.02381.3569115.006276.732910.6562
949.77127.11423.54059.77516.81685.742-0.34130.19341.6167-0.5736-0.37760.1654-2.12490.47110.72851.51380.06730.71350.81450.09861.7482109.878685.82920.8308
954.89215.56514.94926.33015.62975.0025-0.14460.1271.7914-1.5698-0.05361.52-2.2002-1.36720.17791.05740.25250.35330.99440.49831.9478100.7978.92075.9555
964.4589-0.71392.20698.37434.29473.8446-0.3533-1.4066-2.12371.9365-0.37792.13330.5675-0.84640.73461.2561-0.06850.62340.87340.1521.685101.255874.41116.7084
978.50491.4958-1.20118.0274.57085.99980.15590.91270.8068-1.16820.6407-0.261-0.8445-0.2785-0.79560.7081-0.0459-0.08050.73590.38550.9384119.231480.6625-38.5149
988.13285.53957.54727.777.35158.23790.1823-0.1339-0.386-0.06420.03130.35010.016-0.1614-0.1490.5803-0.0290.06060.75270.26510.9092121.281484.467-35.724
995.8492-6.45165.86897.1571-6.43585.936-0.27021.6655-0.0842-0.0609-0.2555-0.52210.13130.58070.55261.2723-0.12450.0041.3128-0.09091.241137.21885.3415-44.772
1009.5542-2.3165-7.20058.1124-2.00077.28592.5641-1.15334.11852.914-0.8629-2.3642-3.40430.5228-1.65732.5454-0.11890.71880.6797-0.04781.8469179.6717139.9111-64.2299
1018.8797-6.4638-6.95984.76415.14035.6021-1.1187-0.2122-0.4846-3.42180.94540.61-1.73090.18580.14333.00440.38220.96781.05710.35412.3832174.0465141.0631-71.6593
1025.928-3.5544-5.5852.23583.34695.2560.01060.1983-0.4733-1.179-0.8005-3.07730.31881.28430.81150.83580.17470.21871.57260.16251.4652171.5727129.1547-77.1239
1032.79932.87192.83232.94822.92213.0242-0.1141.57112.344-1.42430.83720.8347-3.49930.6671-0.78861.20670.04570.5621.01150.52311.5291180.3822132.9727-74.6881
1045.9139-1.7423-5.22565.41915.17777.82960.9609-1.80651.68921.0550.5512-4.0426-1.94574.091-1.36510.9005-0.1548-0.08121.3536-0.14541.162185.5789128.426-66.3004
1059.342-5.954-6.00244.55714.27374.10281.2197-0.18591.13070.23220.2587-0.3066-0.865-0.66-1.38950.895-0.02840.28620.99910.19280.9384174.8899126.9684-67.3392
1065.79255.79746.14695.81396.17418.24190.66971.0408-1.1370.79230.8046-2.08860.10450.8611-1.46550.98090.1291-0.01831.0175-0.16561.4943192.1339126.0287-71.0964
1076.25375.2264-5.45659.0757-7.83719.1941-1.29713.5778-0.1664-2.23771.09121.12622.2018-3.29020.10721.1459-0.1581-0.36442.6829-0.46031.6198250.328112.426927.6956
1089.8196-4.8521.33129.6423.09842.1314-2.009-4.2124-0.2684.14431.56370.8835-1.3083-2.52570.40631.61610.1754-0.0823.1016-0.17630.8743249.282799.013742.2136
1097.1522-5.18065.25893.7485-3.80583.8577-1.25840.73180.81821.72610.4534-2.4717-0.06620.25880.86161.1775-0.2802-0.2822.04490.02351.2792244.64692.429137.1952
1100.2268-0.9683-1.36688.67256.60598.3601-0.3953-3.64460.34860.8742-0.1430.8297-0.3691-2.41730.6140.99010.2807-0.23073.4246-0.0881.1975245.2783104.219829.4627
1112.338-3.66542.95817.5759-4.95013.8111-0.0886-1.9262-0.41890.3781-0.0209-1.0193-0.4202-0.40240.07911.0555-0.0508-0.05841.8466-0.11041.0281248.086895.683929.0612
1129.9111-2.43396.97287.7161-0.66235.0578-1.19491.2648-0.6751-0.45670.5095-1.4584-0.22862.1570.64261.1672-0.15910.16921.77660.0531.4818239.592796.599417.9312
1135.2132-1.77095.25462.2878-1.84165.05620.5363-0.1010.042-0.1334-0.0460.37560.8203-0.0274-0.49651.0688-0.06770.25630.61690.16151.1826107.202141.789-20.2848
1141.6427-2.7953.76085.049-6.80519.17041.27761.97771.62-0.3208-0.69670.8708-0.694-0.71-0.58530.90090.20290.18211.58870.23821.2234105.06651.3499-15.0978
1156.82736.86636.47647.36217.29517.4901-1.03041.32040.6275-0.4872-0.0851-0.0833-2.39612.681.05940.9466-0.27-0.05521.06780.58791.5766102.367452.3154-31.6096
1165.9826-4.7619-3.82244.13763.32934.3072-0.4796-0.6059-0.724-1.5028-1.64222.45220.6678-2.74471.88311.0583-0.2441-0.12021.1986-0.0911.755691.898348.0925-39.3394
1176.1554-7.1691-4.43328.51935.64326.7566-0.9183-1.51550.26593.22540.98450.3947-0.42620.9677-0.1691.2331-0.20750.16821.6571-0.82931.7735249.9095123.92652.766
1184.33061.95134.34242.0091.96684.3556-0.1204-0.87342.5424-1.65570.12610.1384-1.20620.7010.01311.0192-0.0708-0.13710.8332-0.33041.614246.3176129.10464.1176
1194.2215-3.8874-0.81854.5662-0.63942.4020.2514-2.90182.56773.74950.1499-3.1244-1.37551.7263-0.37491.7693-0.4804-0.28352.1687-0.60651.7362252.4432132.546610.2339
1207.052-2.8968-5.2063.56683.03524.178-0.873-3.74215.03481.82944.3168-6.0092-0.13583.1558-3.31371.27320.0069-0.25122.1383-0.63292.1038191.5303102.9786-1.2941
1219.6683-3.0215-2.91795.19455.20345.20781.2239-1.21310.97091.636-0.2164-3.63511.68483.043-1.03111.63480.126-0.25943.027-0.45482.1143204.533395.0084.1886
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 'a' and (resseq 1:6)a1 - 6
121X-RAY DIFFRACTION121chain 'b' and (resseq 30:40)b30 - 40

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