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- PDB-4ylo: E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA -

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Basic information

Entry
Database: PDB / ID: 4ylo
TitleE. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • NT strand DNA (49-MER)
  • RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')
  • RNA polymerase sigma factor RpoD
  • T strand DNA (49-MER)
KeywordsTRANSCRIPTION/DNA/RNA / RNA Polymerase / Initiation Complex / DNA Bubble / TRANSCRIPTION-DNA-RNA complex
Function / homology
Function and homology information


sigma factor antagonist complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex ...sigma factor antagonist complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 ...RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 6 Å
AuthorsZuo, Y. / Steitz, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM057510 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.
Authors: Zuo, Y. / Steitz, T.A.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
1: NT strand DNA (49-MER)
2: T strand DNA (49-MER)
3: RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
4: NT strand DNA (49-MER)
5: T strand DNA (49-MER)
6: RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')
M: DNA-directed RNA polymerase subunit alpha
N: DNA-directed RNA polymerase subunit alpha
O: DNA-directed RNA polymerase subunit beta
P: DNA-directed RNA polymerase subunit beta'
Q: DNA-directed RNA polymerase subunit omega
R: RNA polymerase sigma factor RpoD
7: NT strand DNA (49-MER)
8: T strand DNA (49-MER)
9: RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,422,49736
Polymers1,422,03227
Non-polymers4659
Water00
1
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
1: NT strand DNA (49-MER)
2: T strand DNA (49-MER)
3: RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,16612
Polymers474,0119
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57420 Å2
ΔGint-250 kcal/mol
Surface area185300 Å2
MethodPISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
4: NT strand DNA (49-MER)
5: T strand DNA (49-MER)
6: RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,16612
Polymers474,0119
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58860 Å2
ΔGint-263 kcal/mol
Surface area183470 Å2
MethodPISA
3
M: DNA-directed RNA polymerase subunit alpha
N: DNA-directed RNA polymerase subunit alpha
O: DNA-directed RNA polymerase subunit beta
P: DNA-directed RNA polymerase subunit beta'
Q: DNA-directed RNA polymerase subunit omega
R: RNA polymerase sigma factor RpoD
7: NT strand DNA (49-MER)
8: T strand DNA (49-MER)
9: RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,16612
Polymers474,0119
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58060 Å2
ΔGint-254 kcal/mol
Surface area181960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.888, 208.174, 256.323
Angle α, β, γ (deg.)90.00, 119.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22G
13A
23H
14A
24M
15A
25N
16B
26G
17B
27H
18B
28M
19B
29N
110C
210I
111C
211O
112D
212J
113D
213P
114E
214K
115E
215Q
116F
216L
117F
217R
1181
2184
1191
2197
1202
2205
1212
2218
122G
222H
123G
223M
124G
224N
125H
225M
126H
226N
127I
227O
128J
228P
129K
229Q
130L
230R
1314
2317
1325
2328
133M
233N

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRVALVALAA6 - 23213 - 239
21THRTHRVALVALBB6 - 23213 - 239
12THRTHRARGARGAA6 - 23513 - 242
22THRTHRARGARGGJ6 - 23513 - 242
13THRTHRVALVALAA6 - 23213 - 239
23THRTHRVALVALHK6 - 23213 - 239
14THRTHRARGARGAA6 - 23513 - 242
24THRTHRARGARGMS6 - 23513 - 242
15THRTHRVALVALAA6 - 23213 - 239
25THRTHRVALVALNT6 - 23213 - 239
16THRTHRVALVALBB6 - 23213 - 239
26THRTHRVALVALGJ6 - 23213 - 239
17THRTHRASPASPBB6 - 23313 - 240
27THRTHRASPASPHK6 - 23313 - 240
18THRTHRVALVALBB6 - 23213 - 239
28THRTHRVALVALMS6 - 23213 - 239
19THRTHRASPASPBB6 - 23313 - 240
29THRTHRASPASPNT6 - 23313 - 240
110VALVALGLUGLUCC2 - 13422 - 1342
210VALVALGLUGLUIL2 - 13422 - 1342
111VALVALGLUGLUCC2 - 13422 - 1342
211VALVALGLUGLUOU2 - 13422 - 1342
112GLUGLUGLYGLYDD15 - 137615 - 1376
212GLUGLUGLYGLYJM15 - 137615 - 1376
113GLUGLUGLYGLYDD15 - 137615 - 1376
213GLUGLUGLYGLYPV15 - 137615 - 1376
114ALAALAARGARGEE2 - 911 - 90
214ALAALAARGARGKN2 - 911 - 90
115ALAALAARGARGEE2 - 911 - 90
215ALAALAARGARGQW2 - 911 - 90
116ALAALAASPASPFF79 - 61394 - 628
216ALAALAASPASPLO79 - 61394 - 628
117ALAALAASPASPFF79 - 61394 - 628
217ALAALAASPASPRX79 - 61394 - 628
118DADADCDC1G12 - 601 - 49
218DADADCDC4P12 - 601 - 49
119DADADCDC1G12 - 601 - 49
219DADADCDC7Y12 - 601 - 49
120DGDGDTDT2H3 - 511 - 49
220DGDGDTDT5Q3 - 511 - 49
121DGDGDTDT2H3 - 511 - 49
221DGDGDTDT8Z3 - 511 - 49
122THRTHRVALVALGJ6 - 23213 - 239
222THRTHRVALVALHK6 - 23213 - 239
123THRTHRARGARGGJ6 - 23513 - 242
223THRTHRARGARGMS6 - 23513 - 242
124THRTHRVALVALGJ6 - 23213 - 239
224THRTHRVALVALNT6 - 23213 - 239
125THRTHRVALVALHK6 - 23213 - 239
225THRTHRVALVALMS6 - 23213 - 239
126THRTHRASPASPHK6 - 23313 - 240
226THRTHRASPASPNT6 - 23313 - 240
127VALVALGLUGLUIL2 - 13422 - 1342
227VALVALGLUGLUOU2 - 13422 - 1342
128GLUGLUGLYGLYJM15 - 137615 - 1376
228GLUGLUGLYGLYPV15 - 137615 - 1376
129ALAALAARGARGKN2 - 911 - 90
229ALAALAARGARGQW2 - 911 - 90
130ALAALAASPASPLO79 - 61394 - 628
230ALAALAASPASPRX79 - 61394 - 628
131DADADCDC4P12 - 601 - 49
231DADADCDC7Y12 - 601 - 49
132DGDGDTDT5Q3 - 511 - 49
232DGDGDTDT8Z3 - 511 - 49
133THRTHRVALVALMS6 - 23213 - 239
233THRTHRVALVALNT6 - 23213 - 239

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 15 molecules ABGHMNCIODJPEKQ

#1: Protein
DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 26899.572 Da / Num. of mol.: 6 / Fragment: N-terminal domain (UNP residues 1-235)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, EcE24377A_3778 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7ZSI4, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, EcE24377A_4528 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7ZUK1, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, EcE24377A_4529 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A7ZUK2, UniProt: P0A8T7*PLUS, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10118.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, EcE24377A_4152 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7ZTK1, DNA-directed RNA polymerase

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DNA chain , 2 types, 6 molecules 147258

#6: DNA chain NT strand DNA (49-MER)


Mass: 15024.630 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain T strand DNA (49-MER)


Mass: 15233.764 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / RNA chain , 2 types, 6 molecules FLR369

#5: Protein RNA polymerase sigma factor RpoD / Sigma-70


Mass: 72206.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoD, alt, b3067, JW3039 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00579
#8: RNA chain RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')


Mass: 1440.785 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 9 molecules

#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#10: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 6→40 Å / Num. obs: 55356 / % possible obs: 99.9 % / Redundancy: 5.1 % / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 6→39.95 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.883 / SU B: 837.557 / SU ML: 3.274 / Cross valid method: THROUGHOUT / ESU R Free: 2.584 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31429 2938 5.3 %RANDOM
Rwork0.22687 ---
obs0.23151 52375 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 238.425 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å2-1.28 Å2
2--1.6 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 6→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms88284 6315 9 0 94608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01996649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.914131800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.637511223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.49124.1074215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.9511516674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.12315831
X-RAY DIFFRACTIONr_chiral_restr0.1170.214700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02170245
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2370.14
12B2370.14
21A2650.16
22G2650.16
31A2350.16
32H2350.16
41A2690.17
42M2690.17
51A2460.18
52N2460.18
61B2370.17
62G2370.17
71B2520.11
72H2520.11
81B2390.18
82M2390.18
91B2610.13
92N2610.13
101C16700.14
102I16700.14
111C16860.14
112O16860.14
121D16870.15
122J16870.15
131D16670.14
132P16670.14
141E1020.15
142K1020.15
151E1020.12
152Q1020.12
161F6410.11
162L6410.11
171F6430.12
172R6430.12
18112170.16
18242170.16
19112220.12
19272220.12
20122070.1
20252070.1
21122110.12
21282110.12
221G2390.19
222H2390.19
231G2630.16
232M2630.16
241G2470.19
242N2470.19
251H2350.18
252M2350.18
261H2600.13
262N2600.13
271I16690.14
272O16690.14
281J16330.13
282P16330.13
291K1050.09
292Q1050.09
301L6250.11
302R6250.11
31142180.12
31272180.12
32152010.12
32282010.12
331M2420.2
332N2420.2
LS refinement shellResolution: 6→6.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 252 -
Rwork0.376 3746 -
obs--99.95 %
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)
112.77090.9091-3.934.08161.53917.07520.40890.14320.86160.09650.0078-0.3084-0.32930.1684-0.41682.00870.2570.01930.62550.41341.7128-15.47497.088-66.418
22.00581.53242.10966.86151.24794.2712-0.25661.1265-0.011-0.0365-0.18980.0222-0.03120.57030.44631.89890.41650.11081.6258-0.06132.1442-43.30893.674-42.381
326.4428-4.4936-1.13075.6301-0.58411.46691.07690.2398-0.7641-0.0063-0.61060.73740.0891-0.1405-0.46642.0512-0.2051-0.0651.74010.26811.48112.16591.772-90.712
45.20751.6304-1.56562.5807-0.45063.3617-0.02510.5241-0.5215-0.96430.29680.32630.582-1.1604-0.27172.5682-0.0472-0.1590.44330.24681.5277-29.04458.044-58.496
54.6604-2.0886-1.49046.8187-0.36253.65240.06790.3778-0.38940.0323-0.06480.13360.18040.6313-0.00311.9887-0.0442-0.22650.2377-0.02540.71388.51959.634-34.087
67.1214-1.244110.86011.5194-0.852917.4963-0.1884-0.2454-0.3988-1.0701-0.82051.7341-1.0902-0.71491.0093.7696-0.0216-0.22432.279-0.42793.2872-20.87857.115-29.561
74.2515-2.03491.64372.52260.77223.06530.62430.16030.24490.7339-0.36770.78850.8917-0.8498-0.25663.4307-0.15940.37481.16640.13923.4542-53.42676.343-19.58
81.63010.3126-0.51942.24980.67631.04950.3201-0.5381.02980.21940.29260.4101-0.6188-0.4346-0.61263.9250.23720.37281.2308-0.0472.8325-13.05984.6514.7
91.4660.3283-1.67517.3334-7.03318.601-0.876-1.4774-0.15250.90410.60251.07540.54240.21620.27353.08050.02070.28782.3566-0.66092.9352-50.94542.317-14.102
101.480.3998-4.01739.3427-4.685113.12970.2038-0.5528-0.11420.1236-0.13840.7584-0.36880.6312-0.06542.0457-0.5482-0.14481.1590.00111.7221-30.2114.181-26.141
113.07920.8694-2.04370.4161-0.61191.36780.14930.2479-0.51180.2789-0.4526-0.3826-0.1247-0.0140.30333.7399-0.3269-0.37862.0775-0.15582.1705-29.465-16.202-38.772
1248.912-4.62548.74140.495-1.494911.34580.7610.2054-0.6238-0.2911-0.03190.21131.8084-0.9447-0.72922.75030.5740.39650.8217-0.59442.485115.73310.6-46.217
132.86070.4953-1.44222.2639-0.07734.0146-0.0693-0.1542-0.59181.3294-0.04830.45181.5299-0.56510.11773.9586-0.11620.00940.160.19151.5462-12.58636.812.392
140.6476-0.494-0.34282.328-3.11626.2814-0.5657-1.78420.51480.22131.3305-0.7360.7430.7916-0.76494.33111.07720.14865.1305-0.62855.3582-3.20930.79245.562
154.0943-1.8432-2.24641.18550.56342.41890.3788-1.0365-0.5057-0.703-0.01250.95480.9595-0.0183-0.36644.4716-0.3473-0.37953.7108-0.3913.5890.35913.658-63.23
163.1289-0.379-1.7790.0777-0.203112.9014-0.1679-0.09140.0421-0.10470.10080.0822-0.5889-1.34320.06712.28370.3258-0.15381.1365-0.23712.4314-113.47323.452-75.75
1717.1317-2.4323-1.21684.4651-6.418610.9085-0.8441-0.56550.6420.48990.9286-0.0995-0.3854-1.0379-0.08452.3388-0.09940.10110.7847-0.46011.7157-81.12421.62-58.87
187.75391.76994.41291.11612.85257.6197-0.8355-0.28680.3626-0.264-0.34330.3258-0.2996-1.60361.17882.7469-0.0297-0.08462.2122-0.10413.3704-146.3416.669-91.179
195.1666-0.83081.1033.1226-0.90182.77030.2273-1.0299-0.35330.4730.27531.2332-0.3109-0.8176-0.50272.35430.15960.49220.6284-0.20071.3395-100.521-14.719-64.177
205.52490.64481.54066.24070.92762.48890.13540.46970.15450.08570.270.43270.3008-0.9382-0.40532.22490.10580.28440.6980.24050.8415-92.496-15.147-108.029
215.79870.0749-9.86124.82182.680618.62340.2356-0.528-0.22632.0218-0.5349-0.23141.4810.75560.29933.19040.3388-0.29851.31840.08482.4894-76.748-16.587-83.321
222.5301-0.4982-0.08940.71211.59246.8661-0.0457-1.12210.30020.2768-0.0496-0.13740.28080.52420.09522.894-0.48660.09381.24810.09161.7021-55.5444.45-57.217
231.27271.29850.12172.00730.2381.2636-0.2566-0.64170.40940.0467-0.4225-0.602-0.69250.71770.67913.6458-0.04690.06010.87440.03042.6651-39.14710.84-107.481
249.2141-3.4219-1.18627.42920.03453.8295-0.3384-0.38950.14510.16050.3027-0.78030.20251.42510.03581.8947-0.1945-0.05460.9377-0.07851.0547-50.156-29.729-60.056
2519.8966-2.13551.11865.12260.89645.1295-0.27930.8470.9661-0.205-0.2777-0.42450.7290.12470.55712.2207-0.15850.21250.36810.46371.3565-69.439-58.567-73.344
269.0211-5.0423-2.33194.4894-1.55666.74390.6935-1.04420.0241-0.77480.36130.42510.2470.38-1.05492.4379-0.27140.04471.1958-0.02842.1964-82.634-89.067-68.981
2713.4052-3.27615.729315.3158.51839.52070.4409-1.3891-1.42161.2130.1815-0.06231.2672-0.4707-0.62253.165-0.7684-0.05420.83390.03181.9148-105.974-64.046-107.199
285.6195-0.64380.55693.3544-0.40572.54740.1853-0.2604-1.1496-0.258-0.1759-1.35970.51220.1466-0.00932.75380.0840.51990.04190.22631.8139-50.216-37.12-101.649
290.5721-0.0456-1.21480.51991.06675.0524-0.7725-0.2909-0.2709-0.9250.8639-0.1869-0.96141.3046-0.09154.2184-0.0087-0.08572.8238-0.32893.5413-14.133-44.398-125.118
300.96190.59081.69080.53831.3013.4919-0.47820.44930.77050.1869-0.27620.41330.03370.2380.75443.4464-0.11560.19443.51420.47753.7801-114.38-59.677-87.005
319.40651.7103-3.45562.629-4.10215.0779-0.76941.13820.20940.55960.3040.36260.03530.02140.46531.96590.18690.06150.4481-0.2691.7094-187.38766.982-17.589
3211.46266.5629-1.3937.69482.85355.3632-0.7093-0.31890.7592-0.80280.4819-0.3362-0.4298-0.28210.22751.7010.10420.04151.0899-0.53211.2129-180.40761.30417.983
3311.55745.7212-1.98464.7834-2.903513.4505-0.8250.26940.99580.45190.48561.0608-0.12740.32380.33931.98060.3622-0.0351.3860.43771.6585-195.2464.382-53.154
343.3593-0.0305-0.20024.0349-2.14635.2766-0.0066-0.6276-0.2124-0.33980.07410.94330.6742-0.2032-0.06752.07720.2174-0.09540.1632-0.02360.8822-184.92326.92-4.996
352.5871-0.48810.99036.7018-0.64755.7804-0.02871.00850.1258-0.2366-0.1284-0.32770.41190.08540.15721.43520.10180.22140.68720.33531.389-145.51433.099-25.531
3669.3948-31.02975.794214.3772-2.54620.50040.42991.02370.5840.437-0.64940.6902-0.07360.07590.21953.0366-0.46570.0411.2997-0.25382.4022-155.65327.4371.998
379.59880.6596-6.49752.8203-1.09415.67610.2451-1.41710.34990.0843-0.353-0.3191-0.24720.63170.1081.8229-0.3234-0.45141.3035-0.2271.437-164.16943.11836.494
381.48562.33-1.41554.4939-1.92211.71050.5366-0.30090.38381.22360.10340.4568-0.781-0.0073-0.644.1547-0.42250.02942.1177-0.06452.7489-115.59256.74119.806
393.852-4.48153.08326.2206-3.21595.5891-0.1816-0.3019-0.25451.055-0.3542-0.28221.04331.39020.53572.04960.0678-0.22782.19380.28331.9225-156.19.54535.162
406.0471-4.36593.43954.6598-0.538410.7471-0.5990.0436-0.47780.37430.293-0.8183-0.1771.0570.30591.80270.04120.11330.79330.0992.4003-154.286-15.858.08
410.18280.1763-0.46974.2504-6.34049.70180.41050.2837-0.3428-0.8437-0.21150.42080.715-0.0074-0.19912.56160.1166-0.40991.8983-0.09963.2623-161.614-45.65-3.786
4214.2496-8.54678.73417.8701-3.67056.4720.5386-0.2262-1.42470.94020.40590.56390.57230.4402-0.94462.6789-0.16720.31631.7363-0.29142.2619-147.869-15.669-40.335
431.761-0.46750.76033.238-0.29874.72750.2374-0.4703-1.13010.484-0.1869-0.88290.57560.0468-0.05062.37910.0855-0.32321.42190.25282.797-122.388.8519.277
443.8205-1.23980.7430.6952-0.01190.3643-0.0529-0.6291-0.4923-0.79460.8535-0.4169-0.38540.4824-0.80064.69370.12630.80133.9864-0.38243.7037-80.7673.75422.669
454.0571-1.3091-1.29820.77510.27050.8128-0.00180.4198-0.50430.1419-1.06290.048-0.62480.56731.06464.6975-0.3462-0.27773.81310.1393.9142-171.948-14.463-35.501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 51
2X-RAY DIFFRACTION1A179 - 235
3X-RAY DIFFRACTION1B6 - 51
4X-RAY DIFFRACTION1B179 - 233
5X-RAY DIFFRACTION2A52 - 178
6X-RAY DIFFRACTION3B52 - 178
7X-RAY DIFFRACTION4C2 - 28
8X-RAY DIFFRACTION4C146 - 152
9X-RAY DIFFRACTION4C445 - 455
10X-RAY DIFFRACTION4C517 - 831
11X-RAY DIFFRACTION4C1057 - 1241
12X-RAY DIFFRACTION4D501 - 790
13X-RAY DIFFRACTION5C1242 - 1320
14X-RAY DIFFRACTION5D343 - 500
15X-RAY DIFFRACTION5D791 - 943
16X-RAY DIFFRACTION5D1129 - 1153
17X-RAY DIFFRACTION5D1213 - 1317
18X-RAY DIFFRACTION5D1345 - 1376
19X-RAY DIFFRACTION5D1502 - 1503
20X-RAY DIFFRACTION5E2 - 91
21X-RAY DIFFRACTION5F505 - 529
22X-RAY DIFFRACTION6213 - 22
23X-RAY DIFFRACTION6313 - 16
24X-RAY DIFFRACTION7C832 - 891
25X-RAY DIFFRACTION7C912 - 1056
26X-RAY DIFFRACTION8C892 - 911
27X-RAY DIFFRACTION8F530 - 613
28X-RAY DIFFRACTION8112 - 36
29X-RAY DIFFRACTION8227 - 51
30X-RAY DIFFRACTION9C29 - 145
31X-RAY DIFFRACTION9C456 - 516
32X-RAY DIFFRACTION10C153 - 226
33X-RAY DIFFRACTION10C337 - 444
34X-RAY DIFFRACTION10147 - 51
35X-RAY DIFFRACTION11C227 - 336
36X-RAY DIFFRACTION12D1154 - 1212
37X-RAY DIFFRACTION13C1321 - 1342
38X-RAY DIFFRACTION13D15 - 342
39X-RAY DIFFRACTION13D1318 - 1344
40X-RAY DIFFRACTION13D1501
41X-RAY DIFFRACTION13F79 - 136
42X-RAY DIFFRACTION13F356 - 504
43X-RAY DIFFRACTION13137 - 46
44X-RAY DIFFRACTION13223 - 26
45X-RAY DIFFRACTION13152 - 60
46X-RAY DIFFRACTION1323 - 12
47X-RAY DIFFRACTION14F137 - 355
48X-RAY DIFFRACTION15D944 - 1128
49X-RAY DIFFRACTION16G6 - 51
50X-RAY DIFFRACTION16G179 - 235
51X-RAY DIFFRACTION16H6 - 51
52X-RAY DIFFRACTION16H179 - 233
53X-RAY DIFFRACTION17G52 - 178
54X-RAY DIFFRACTION18H52 - 178
55X-RAY DIFFRACTION19I2 - 28
56X-RAY DIFFRACTION19I146 - 152
57X-RAY DIFFRACTION19I445 - 455
58X-RAY DIFFRACTION19I517 - 831
59X-RAY DIFFRACTION19I1057 - 1241
60X-RAY DIFFRACTION19J501 - 790
61X-RAY DIFFRACTION20I1242 - 1320
62X-RAY DIFFRACTION20J343 - 500
63X-RAY DIFFRACTION20J791 - 943
64X-RAY DIFFRACTION20J1129 - 1153
65X-RAY DIFFRACTION20J1213 - 1317
66X-RAY DIFFRACTION20J1345 - 1376
67X-RAY DIFFRACTION20J1502 - 1503
68X-RAY DIFFRACTION20K2 - 91
69X-RAY DIFFRACTION20L505 - 529
70X-RAY DIFFRACTION21513 - 22
71X-RAY DIFFRACTION21613 - 16
72X-RAY DIFFRACTION22I832 - 891
73X-RAY DIFFRACTION22I912 - 1056
74X-RAY DIFFRACTION23I892 - 911
75X-RAY DIFFRACTION23L530 - 613
76X-RAY DIFFRACTION23412 - 36
77X-RAY DIFFRACTION23527 - 51
78X-RAY DIFFRACTION24I29 - 145
79X-RAY DIFFRACTION24I456 - 516
80X-RAY DIFFRACTION25I153 - 226
81X-RAY DIFFRACTION25I337 - 444
82X-RAY DIFFRACTION25447 - 51
83X-RAY DIFFRACTION26I227 - 336
84X-RAY DIFFRACTION27J1154 - 1212
85X-RAY DIFFRACTION28I1321 - 1342
86X-RAY DIFFRACTION28J15 - 342
87X-RAY DIFFRACTION28J1318 - 1344
88X-RAY DIFFRACTION28J1501
89X-RAY DIFFRACTION28L79 - 136
90X-RAY DIFFRACTION28L356 - 504
91X-RAY DIFFRACTION28437 - 45
92X-RAY DIFFRACTION28523 - 26
93X-RAY DIFFRACTION28452 - 60
94X-RAY DIFFRACTION2853 - 12
95X-RAY DIFFRACTION29L137 - 355
96X-RAY DIFFRACTION30J944 - 1128
97X-RAY DIFFRACTION31M6 - 51
98X-RAY DIFFRACTION31M179 - 235
99X-RAY DIFFRACTION31N6 - 51
100X-RAY DIFFRACTION31N179 - 233
101X-RAY DIFFRACTION32M52 - 178
102X-RAY DIFFRACTION33N52 - 178
103X-RAY DIFFRACTION34O2 - 28
104X-RAY DIFFRACTION34O146 - 152
105X-RAY DIFFRACTION34O445 - 455
106X-RAY DIFFRACTION34O517 - 831
107X-RAY DIFFRACTION34O1057 - 1241
108X-RAY DIFFRACTION34P501 - 790
109X-RAY DIFFRACTION35O1242 - 1320
110X-RAY DIFFRACTION35P343 - 500
111X-RAY DIFFRACTION35P791 - 943
112X-RAY DIFFRACTION35P1129 - 1153
113X-RAY DIFFRACTION35P1213 - 1317
114X-RAY DIFFRACTION35P1345 - 1376
115X-RAY DIFFRACTION35P1502 - 1503
116X-RAY DIFFRACTION35Q2 - 91
117X-RAY DIFFRACTION35R505 - 529
118X-RAY DIFFRACTION36813 - 22
119X-RAY DIFFRACTION36913 - 16
120X-RAY DIFFRACTION37O832 - 891
121X-RAY DIFFRACTION37O912 - 1056
122X-RAY DIFFRACTION38O892 - 911
123X-RAY DIFFRACTION38R530 - 613
124X-RAY DIFFRACTION38712 - 36
125X-RAY DIFFRACTION38827 - 51
126X-RAY DIFFRACTION39O29 - 145
127X-RAY DIFFRACTION39O456 - 516
128X-RAY DIFFRACTION40O153 - 226
129X-RAY DIFFRACTION40O337 - 444
130X-RAY DIFFRACTION40747 - 51
131X-RAY DIFFRACTION41O227 - 336
132X-RAY DIFFRACTION42P1154 - 1212
133X-RAY DIFFRACTION43O1321 - 1342
134X-RAY DIFFRACTION43P15 - 342
135X-RAY DIFFRACTION43P1318 - 1344
136X-RAY DIFFRACTION43P1501
137X-RAY DIFFRACTION43R79 - 136
138X-RAY DIFFRACTION43R356 - 504
139X-RAY DIFFRACTION43737 - 46
140X-RAY DIFFRACTION43823 - 26
141X-RAY DIFFRACTION43752 - 60
142X-RAY DIFFRACTION4383 - 12
143X-RAY DIFFRACTION44R137 - 355
144X-RAY DIFFRACTION45P944 - 1128

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