[English] 日本語
Yorodumi
- PDB-4lk1: Crystal Structure Analysis of the E.coli holoenzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lk1
TitleCrystal Structure Analysis of the E.coli holoenzyme
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
KeywordsTRANSFERASE
Function / homology
Function and homology information


sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / response to heat / negative regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 ...Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / 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 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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 / Helix Hairpins / 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 / Gyrase A; domain 2 / Beta Complex / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Roll / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / : / : / : / RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8369 Å
AuthorsBae, B. / Darst, S.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of sigma 70 domain 1.1.
Authors: Bae, B. / Davis, E. / Brown, D. / Campbell, E.A. / Wigneshweraraj, S. / Darst, S.A.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)879,72618
Polymers879,41512
Non-polymers3106
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,8639
Polymers439,7086
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37480 Å2
ΔGint-178 kcal/mol
Surface area158100 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,8639
Polymers439,7086
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38090 Å2
ΔGint-183 kcal/mol
Surface area163620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.675, 206.392, 308.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resseq 3:30 or resseq 140:150 or resseq...
21(chain I and (resseq 3:30 or resseq 140:150 or resseq...
12chain C and (resseq 31:139 or resseq 456:512)
22chain I and (resseq 31:139 or resseq 456:512)
13chain C and (resseq 151:225 or resseq 340:444)
23chain I and (resseq 151:225 or resseq 340:444)
14chain C and resseq 226:339
24chain I and resseq 226:339
15chain C and resseq 714:785
25chain I and resseq 714:785
16(chain C and (resseq 833:937 or resseq 1040:1055)) or (chain F and resseq 551:612)
26(chain I and (resseq 833:937 or resseq 1040:1055)) or (chain L and resseq 551:612)
17chain C and resseq 938:1039
27chain I and resseq 938:1039
18(chain C and resseq 1296:1342) or (chain D and (resseq...
28(chain I and resseq 1296:1342) or (chain J and (resseq...
19chain F and (resseq 128:167 or resseq 212:236 or resseq 242:374)
29chain L and (resseq 128:167 or resseq 212:236 or resseq 242:374)
110chain F and resseq 445:550
210chain L and resseq 445:550
111chain A and (resseq 9:52 or resseq 179:231)
211chain G and (resseq 9:52 or resseq 179:231)
112chain A and resseq 53:178
212chain G and resseq 53:178
113chain B and (resseq 9:52 or resseq 179:231)
213chain H and (resseq 9:52 or resseq 179:231)
114chain B and resseq 53:178
214chain H and resseq 53:178
115chain F and resseq 7:90
215chain L and resseq 7:90

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'C' and (resseq 3:30 or resseq 140:150 or resseq...C3 - 30
121(chain 'C' and (resseq 3:30 or resseq 140:150 or resseq...C140 - 150
131(chain 'C' and (resseq 3:30 or resseq 140:150 or resseq...C445 - 455
141(chain 'C' and (resseq 3:30 or resseq 140:150 or resseq...C513 - 713
151(chain 'C' and (resseq 3:30 or resseq 140:150 or resseq...C786 - 832
161(chain 'C' and (resseq 3:30 or resseq 140:150 or resseq...C1056 - 1295
211(chain 'I' and (resseq 3:30 or resseq 140:150 or resseq...I3 - 30
221(chain 'I' and (resseq 3:30 or resseq 140:150 or resseq...I140 - 150
231(chain 'I' and (resseq 3:30 or resseq 140:150 or resseq...I445 - 455
241(chain 'I' and (resseq 3:30 or resseq 140:150 or resseq...I513 - 713
251(chain 'I' and (resseq 3:30 or resseq 140:150 or resseq...I786 - 832
261(chain 'I' and (resseq 3:30 or resseq 140:150 or resseq...I1056 - 1295
112chain 'C' and (resseq 31:139 or resseq 456:512)C31 - 139
122chain 'C' and (resseq 31:139 or resseq 456:512)C456 - 512
212chain 'I' and (resseq 31:139 or resseq 456:512)I31 - 139
222chain 'I' and (resseq 31:139 or resseq 456:512)I456 - 512
113chain 'C' and (resseq 151:225 or resseq 340:444)C151 - 225
123chain 'C' and (resseq 151:225 or resseq 340:444)C340 - 444
213chain 'I' and (resseq 151:225 or resseq 340:444)I151 - 225
223chain 'I' and (resseq 151:225 or resseq 340:444)I340 - 444
114chain 'C' and resseq 226:339C226 - 339
214chain 'I' and resseq 226:339I226 - 339
115chain 'C' and resseq 714:785C714 - 785
215chain 'I' and resseq 714:785I714 - 785
116(chain 'C' and (resseq 833:937 or resseq 1040:1055)) or (chain 'F' and resseq 551:612)C833 - 937
126(chain 'C' and (resseq 833:937 or resseq 1040:1055)) or (chain 'F' and resseq 551:612)C1040 - 1055
216(chain 'I' and (resseq 833:937 or resseq 1040:1055)) or (chain 'L' and resseq 551:612)I833 - 937
226(chain 'I' and (resseq 833:937 or resseq 1040:1055)) or (chain 'L' and resseq 551:612)I1040 - 1055
117chain 'C' and resseq 938:1039C938 - 1039
217chain 'I' and resseq 938:1039I938 - 1039
118(chain 'C' and resseq 1296:1342) or (chain 'D' and (resseq...C1296 - 1342
218(chain 'I' and resseq 1296:1342) or (chain 'J' and (resseq...I1296 - 1342
119chain 'F' and (resseq 128:167 or resseq 212:236 or resseq 242:374)F128 - 167
129chain 'F' and (resseq 128:167 or resseq 212:236 or resseq 242:374)F212 - 236
139chain 'F' and (resseq 128:167 or resseq 212:236 or resseq 242:374)F242 - 374
219chain 'L' and (resseq 128:167 or resseq 212:236 or resseq 242:374)L128 - 167
229chain 'L' and (resseq 128:167 or resseq 212:236 or resseq 242:374)L212 - 236
239chain 'L' and (resseq 128:167 or resseq 212:236 or resseq 242:374)L242 - 374
1110chain 'F' and resseq 445:550F445 - 550
2110chain 'L' and resseq 445:550L445 - 550
1111chain 'A' and (resseq 9:52 or resseq 179:231)A9 - 52
1211chain 'A' and (resseq 9:52 or resseq 179:231)A179 - 231
2111chain 'G' and (resseq 9:52 or resseq 179:231)G9 - 52
2211chain 'G' and (resseq 9:52 or resseq 179:231)G179 - 231
1112chain 'A' and resseq 53:178A53 - 178
2112chain 'G' and resseq 53:178G53 - 178
1113chain 'B' and (resseq 9:52 or resseq 179:231)B9 - 52
1213chain 'B' and (resseq 9:52 or resseq 179:231)B179 - 231
2113chain 'H' and (resseq 9:52 or resseq 179:231)H9 - 52
2213chain 'H' and (resseq 9:52 or resseq 179:231)H179 - 231
1114chain 'B' and resseq 53:178B53 - 178
2114chain 'H' and resseq 53:178H53 - 178
1115chain 'F' and resseq 7:90F7 - 90
2115chain 'L' and resseq 7:90L7 - 90

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(-0.414931, -0.00594, -0.909833), (-0.039634, -0.998911, 0.024597), (-0.908989, 0.046267, 0.414244)-69.088203, -220.483002, -39.509701
2given(-0.473436, 0.046307, -0.87961), (-0.081993, -0.996598, -0.008334), (-0.877003, 0.068177, 0.475623)-63.981098, -225.975998, -29.165701
3given(-0.360051, 0.0504, -0.93157), (-0.065235, -0.997456, -0.028751), (-0.930649, 0.050419, 0.362422)-59.3475, -226.656006, -44.821899
4given(-0.344287, 0.074381, -0.935913), (-0.085561, -0.995194, -0.047617), (-0.934958, 0.063684, 0.348996)-55.796501, -229.201004, -44.625401
5given(-0.418253, -0.005906, -0.908311), (-0.048645, -0.998398, 0.028892), (-0.907027, 0.056269, 0.417296)-69.358902, -220.906006, -37.581501
6given(-0.440731, -0.00749, -0.897608), (-0.018058, -0.999689, 0.017209), (-0.897458, 0.023793, 0.440458)-70.405098, -219.410004, -41.008801
7given(-0.412511, 0.006519, -0.910929), (-0.046408, -0.998826, 0.013867), (-0.90977, 0.047994, 0.41233)-67.151299, -221.653, -39.489899
8given(-0.425117, 0.005595, -0.905121), (-0.028005, -0.999583, 0.006975), (-0.904705, 0.028313, 0.425096)-67.681297, -220.897995, -41.504299
9given(-0.418817, 0.038329, -0.907261), (0.038257, -0.997477, -0.059801), (-0.907265, -0.059754, 0.416294)-62.143101, -225.106003, -58.001598
10given(-0.428616, -0.00641, -0.903464), (-0.017794, -0.999721, 0.015535), (-0.903312, 0.022734, 0.428382)-69.808998, -219.893005, -42.1367
11given(-0.415288, -0.003746, -0.909682), (-0.03948, -0.998975, 0.022137), (-0.908833, 0.045108, 0.414714)-68.662804, -220.417999, -39.730301
12given(-0.416965, 0.003446, -0.908916), (-0.038392, -0.999167, 0.013824), (-0.908111, 0.040659, 0.41675)-67.7966, -220.705994, -40.239399
13given(-0.399439, -0.022154, -0.916492), (-0.029083, -0.998899, 0.036822), (-0.916298, 0.041363, 0.398355)-69.694504, -219.011002, -41.308601
14given(-0.383272, -0.060315, -0.921664), (-0.031035, -0.996461, 0.078116), (-0.923114, 0.058544, 0.380044)-72.591698, -218.300995, -40.258801
15given(-0.45577, -0.1072, -0.883619), (-0.052669, -0.987734, 0.146998), (-0.888538, 0.113536, 0.444533)-81.690201, -209.886993, -28.066

-
Components

-
DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABGHCIDJEK

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


Mass: 26459.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoA, EcDH1_0418, ECDH1ME8569_3173 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QXI7, 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoB, EcDH1_4008, ECDH1ME8569_3846 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QV90, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoC, BWG_3647 / Production host: Escherichia coli (E. coli) / References: UniProt: C5A0S8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoZ, EcDH1_0056, ECDH1ME8569_3534 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QUL2, DNA-directed RNA polymerase

-
Protein , 1 types, 2 molecules FL

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


Mass: 70352.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Production host: Escherichia coli (E. coli) / References: UniProt: P00579

-
Non-polymers , 2 types, 6 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, pH 6, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.8369→45 Å / Num. obs: 203945 / % possible obs: 100 % / Redundancy: 17.1 % / Rmerge(I) obs: 0.203 / Χ2: 1.129 / Net I/σ(I): 4
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3.8369-4.0913.2204420.81100
4.09-4.2514.5203870.8261100
4.25-4.4515.6203360.851100
4.45-4.6816.6204420.8681100
4.68-4.9817.6203440.88311000.912
4.98-5.3618.5204260.88411000.839
5.36-5.918.9203480.89411000.695
5.9-6.7518.9203990.93411000.451
6.75-8.4918.7204001.39511000.176
8.49-4518.2204212.7311000.065

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8369→44.781 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7582 / SU ML: 0.54 / σ(F): 1.35 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 5631 5.01 %
Rwork0.2235 --
obs0.226 112428 98.25 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 225.36 Å2 / Biso mean: 102.8943 Å2 / Biso min: 10 Å2
Refinement stepCycle: LAST / Resolution: 3.8369→44.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57164 0 6 0 57170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00458028
X-RAY DIFFRACTIONf_angle_d0.92778338
X-RAY DIFFRACTIONf_chiral_restr0.0678950
X-RAY DIFFRACTIONf_plane_restr0.00410283
X-RAY DIFFRACTIONf_dihedral_angle_d16.7322278
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C11014X-RAY DIFFRACTIONPOSITIONAL0.011
12I11014X-RAY DIFFRACTIONPOSITIONAL0.011
21C1310X-RAY DIFFRACTIONPOSITIONAL0.021
22I1310X-RAY DIFFRACTIONPOSITIONAL0.021
31C1470X-RAY DIFFRACTIONPOSITIONAL0.014
32I1470X-RAY DIFFRACTIONPOSITIONAL0.014
41C912X-RAY DIFFRACTIONPOSITIONAL0.023
42I912X-RAY DIFFRACTIONPOSITIONAL0.023
51C549X-RAY DIFFRACTIONPOSITIONAL0.007
52I549X-RAY DIFFRACTIONPOSITIONAL0.007
61C1414X-RAY DIFFRACTIONPOSITIONAL0.017
62I1414X-RAY DIFFRACTIONPOSITIONAL0.017
71C835X-RAY DIFFRACTIONPOSITIONAL0.015
72I835X-RAY DIFFRACTIONPOSITIONAL0.015
81C4028X-RAY DIFFRACTIONPOSITIONAL0.025
82I4028X-RAY DIFFRACTIONPOSITIONAL0.025
91F1626X-RAY DIFFRACTIONPOSITIONAL0.018
92L1626X-RAY DIFFRACTIONPOSITIONAL0.018
101F836X-RAY DIFFRACTIONPOSITIONAL0.011
102L836X-RAY DIFFRACTIONPOSITIONAL0.011
111A762X-RAY DIFFRACTIONPOSITIONAL0.008
112G762X-RAY DIFFRACTIONPOSITIONAL0.008
121A963X-RAY DIFFRACTIONPOSITIONAL0.007
122G963X-RAY DIFFRACTIONPOSITIONAL0.007
131B762X-RAY DIFFRACTIONPOSITIONAL0.014
132H762X-RAY DIFFRACTIONPOSITIONAL0.014
141B855X-RAY DIFFRACTIONPOSITIONAL0.014
142H855X-RAY DIFFRACTIONPOSITIONAL0.014
151F367X-RAY DIFFRACTIONPOSITIONAL0.042
152L367X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8369-3.88050.38621530.28952913306681
3.8805-3.92610.35881740.2913164333889
3.9261-3.97390.35411660.29283278344491
3.9739-4.02420.40621720.29063301347393
4.0242-4.07710.34851840.28423451363596
4.0771-4.13290.33271800.25813521370199
4.1329-4.19190.33492120.24735843796100
4.1919-4.25450.28891900.232835853775100
4.2545-4.32090.27681960.230935873783100
4.3209-4.39170.30882120.240435613773100
4.3917-4.46730.30171820.23635943776100
4.4673-4.54850.33111860.227935923778100
4.5485-4.63590.26671840.214636103794100
4.6359-4.73040.29092000.219735873787100
4.7304-4.83310.27221840.212236153799100
4.8331-4.94540.27131770.221236303807100
4.9454-5.0690.27821910.220335833774100
5.069-5.20580.27432020.221536203822100
5.2058-5.35880.28741900.223135863776100
5.3588-5.53140.30781730.222636413814100
5.5314-5.72870.29251740.227436583832100
5.7287-5.95760.27772230.236835823805100
5.9576-6.22810.31731620.243536653827100
6.2281-6.55550.31281760.22936383814100
6.5555-6.96480.2791860.233636723858100
6.9648-7.50020.28482000.210236463846100
7.5002-8.25080.21751970.19536693866100
8.2508-9.43490.19422000.178736863886100
9.4349-11.85050.19041870.17737243911100
11.8505-44.78430.27262180.252638544072100

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

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

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

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

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

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

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

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

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

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

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

+
Jul 12, 2017. Major update of PDB

Major update of PDB

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

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

-
Yorodumi

Thousand views of thousand structures

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

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

Read more