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- PDB-4lk0: Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex -

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Basic information

Entry
Database: PDB / ID: 4lk0
TitleCrystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • Bacterial RNA polymerase inhibitor
  • RNA polymerase sigma factor RpoD
KeywordsTRANSFERASE / DNA directed RNA polymerase
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / 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
RNA polymerase inhibitor / RNA polymerase inhibitor / RNA polymerase inhibitor superfamily / RNA polymerase inhibitor / Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / 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 inhibitor / RNA polymerase inhibitor / RNA polymerase inhibitor superfamily / RNA polymerase inhibitor / Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / 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 sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase II, Rpb2 subunit, wall domain / 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 / Sigma-70 factors family signature 1. / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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 / Helix Hairpins / Gyrase A; domain 2 / Beta Complex / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Roll / Winged helix-like DNA-binding domain superfamily / Roll / 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 / Bacterial RNA polymerase inhibitor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9103 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

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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
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
M: Bacterial RNA polymerase inhibitor
N: Bacterial RNA polymerase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)874,01420
Polymers873,70314
Non-polymers3106
Water0
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
M: Bacterial RNA polymerase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,00710
Polymers436,8527
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39190 Å2
ΔGint-184 kcal/mol
Surface area164420 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
N: Bacterial RNA polymerase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,00710
Polymers436,8527
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38900 Å2
ΔGint-187 kcal/mol
Surface area163500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.364, 206.283, 307.999
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 938:955
27chain I and resseq 938:955
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 M
215chain N
116chain D and resseq 948:1022
216chain J and resseq 948:1022
117chain D and resseq 1023:1126
217chain J and resseq 1023:1126

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 938:955C938 - 955
217chain 'I' and resseq 938:955I938 - 955
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 MM13 - 63
2115chain NN13 - 63
1116chain D and resseq 948:1022D948 - 1022
2116chain J and resseq 948:1022J948 - 1022
1117chain D and resseq 1023:1126D1023 - 1126
2117chain J and resseq 1023:1126J1023 - 1126

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17

NCS oper:
IDCodeMatrixVector
1given(-0.407519, -0.003261, -0.913191), (-0.034797, -0.999212, 0.019097), (-0.912533, 0.039559, 0.407085)-69.324402, -220.591003, -40.814098
2given(-0.462831, 0.038474, -0.885611), (-0.073743, -0.997266, -0.004786), (-0.883374, 0.063092, 0.464402)-65.681702, -225.214996, -30.7292
3given(-0.354551, 0.073198, -0.932167), (-0.076535, -0.995858, -0.049089), (-0.931899, 0.053939, 0.358684)-56.737999, -228.994003, -44.303101
4given(-0.322479, 0.096819, -0.941612), (-0.092597, -0.993211, -0.070413), (-0.942037, 0.064484, 0.329254)-53.098499, -231.654999, -46.3638
5given(-0.408227, -0.007285, -0.912851), (-0.041035, -0.998811, 0.026322), (-0.911958, 0.048205, 0.407443)-70.091904, -220.503998, -39.494499
6given(-0.430594, -0.003199, -0.90254), (-0.021643, -0.99967, 0.013869), (-0.902286, 0.025505, 0.430383)-70.330498, -219.992004, -41.2803
7given(-0.391141, -0.028555, -0.919888), (-0.039579, -0.998072, 0.047811), (-0.919479, 0.055109, 0.389256)-73.1577, -219.098999, -39.670101
8given(-0.41429, 0.006768, -0.91012), (-0.025301, -0.999672, 0.004083), (-0.909793, 0.024718, 0.414325)-67.881897, -221.003998, -42.542
9given(-0.410644, 0.023016, -0.911505), (0.041653, -0.998164, -0.043969), (-0.910844, -0.056022, 0.408931)-65.328003, -223.940994, -57.2174
10given(-0.421125, -0.01117, -0.906934), (-0.008085, -0.999838, 0.016068), (-0.906967, 0.014099, 0.420966)-71.017601, -219.533005, -43.693501
11given(-0.41341, -0.012303, -0.910462), (-0.027891, -0.999268, 0.026167), (-0.910118, 0.036212, 0.412764)-70.831902, -219.630997, -40.858002
12given(-0.411677, 0.006793, -0.911305), (-0.035745, -0.999323, 0.008698), (-0.910629, 0.036155, 0.411641)-67.9767, -220.927002, -40.931099
13given(-0.404011, -0.010029, -0.914699), (-0.026708, -0.999384, 0.022754), (-0.914364, 0.033622, 0.403494)-69.738403, -219.436996, -42.0158
14given(-0.404703, -0.062904, -0.912282), (-0.009805, -0.997275, 0.073114), (-0.914396, 0.038534, 0.402984)-76.1856, -216.591995, -41.4067
15given(-0.421184, -0.056418, -0.905219), (-0.03775, -0.996108, 0.079647), (-0.906189, 0.067718, 0.417415)-74.920303, -216.069, -36.785198
16given(-0.406131, -0.029949, -0.913324), (-0.021522, -0.998872, 0.042325), (-0.913561, 0.036846, 0.405028)-71.798103, -218.410995, -41.501099
17given(-0.402428, -0.02977, -0.914967), (-0.019247, -0.998975, 0.040969), (-0.915249, 0.034097, 0.401443)-71.741997, -218.380005, -42.056499

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Components

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

#1: Protein
DNA-directed RNA polymerase subunit alpha / Polymerase / 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 / Polymerase / 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' / Polymerase


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 / Polymerase / 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

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Protein , 2 types, 4 molecules FLMN

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


Mass: 60315.254 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
#6: Protein Bacterial RNA polymerase inhibitor


Mass: 7180.985 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Gene: 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03704

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Non-polymers , 2 types, 6 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


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


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.9→40 Å / Num. obs: 103109 / % possible obs: 96.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.176 / Χ2: 1.417 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3.9-4.046.9100650.965195.2
4.04-4.27102501.028196.80.834
4.2-4.397103351.121197.40.6
4.39-4.627.1102961.174197.20.457
4.62-4.917.1103241.203197.20.37
4.91-5.297.1103411.186196.80.331
5.29-5.827.2102761.216196.70.28
5.82-6.667.2103571.386196.30.208
6.66-8.386.9103522.233195.80.108
8.38-406.3105132.798194.30.046

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9103→39.941 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7697 / SU ML: 0.54 / σ(F): 1.35 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 5023 5.03 %RANDOM
Rwork0.2189 ---
obs0.221 99877 92.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.85 Å2 / Biso mean: 82.345 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 3.9103→39.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58499 0 6 0 58505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00459407
X-RAY DIFFRACTIONf_angle_d0.91380202
X-RAY DIFFRACTIONf_chiral_restr0.0659145
X-RAY DIFFRACTIONf_plane_restr0.00410512
X-RAY DIFFRACTIONf_dihedral_angle_d17.3922870
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C11014X-RAY DIFFRACTIONPOSITIONAL0.02
12I11014X-RAY DIFFRACTIONPOSITIONAL0.02
21C1310X-RAY DIFFRACTIONPOSITIONAL0.021
22I1310X-RAY DIFFRACTIONPOSITIONAL0.021
31C1470X-RAY DIFFRACTIONPOSITIONAL0.017
32I1470X-RAY DIFFRACTIONPOSITIONAL0.017
41C912X-RAY DIFFRACTIONPOSITIONAL0.007
42I912X-RAY DIFFRACTIONPOSITIONAL0.007
51C549X-RAY DIFFRACTIONPOSITIONAL0.007
52I549X-RAY DIFFRACTIONPOSITIONAL0.007
61C1414X-RAY DIFFRACTIONPOSITIONAL0.013
62I1414X-RAY DIFFRACTIONPOSITIONAL0.013
71C148X-RAY DIFFRACTIONPOSITIONAL0.013
72I148X-RAY DIFFRACTIONPOSITIONAL0.013
81C3954X-RAY DIFFRACTIONPOSITIONAL0.015
82I3954X-RAY DIFFRACTIONPOSITIONAL0.015
91F1626X-RAY DIFFRACTIONPOSITIONAL0.018
92L1626X-RAY DIFFRACTIONPOSITIONAL0.018
101F836X-RAY DIFFRACTIONPOSITIONAL0.01
102L836X-RAY DIFFRACTIONPOSITIONAL0.01
111A762X-RAY DIFFRACTIONPOSITIONAL0.009
112G762X-RAY DIFFRACTIONPOSITIONAL0.009
121A963X-RAY DIFFRACTIONPOSITIONAL0.005
122G963X-RAY DIFFRACTIONPOSITIONAL0.005
131B762X-RAY DIFFRACTIONPOSITIONAL0.024
132H762X-RAY DIFFRACTIONPOSITIONAL0.024
141B855X-RAY DIFFRACTIONPOSITIONAL0.024
142H855X-RAY DIFFRACTIONPOSITIONAL0.024
151M413X-RAY DIFFRACTIONPOSITIONAL0.007
152N413X-RAY DIFFRACTIONPOSITIONAL0.007
161D562X-RAY DIFFRACTIONPOSITIONAL0.005
162J562X-RAY DIFFRACTIONPOSITIONAL0.005
171D778X-RAY DIFFRACTIONPOSITIONAL0.005
172J778X-RAY DIFFRACTIONPOSITIONAL0.005
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 (%)
3.9103-3.95470.43551230.31622323244669
3.9547-4.00120.36621570.30472724288181
4.0012-4.04990.35751370.3082789292683
4.0499-4.10110.34611580.292849300785
4.1011-4.1550.32971540.27612950310487
4.155-4.21190.29971640.27462991315589
4.2119-4.2720.38111710.2633016318790
4.272-4.33570.28891760.25063084326092
4.3357-4.40340.27991740.26243157333194
4.4034-4.47550.33211670.24623233340095
4.4755-4.55250.29551700.24133198336895
4.5525-4.63520.3121660.23643254342096
4.6352-4.72420.27861790.23643246342597
4.7242-4.82050.29611690.2233275344497
4.8205-4.92510.2671650.22373299346497
4.9251-5.03950.30281800.22633290347097
5.0395-5.16520.2741860.22473278346497
5.1652-5.30460.2771720.21323284345697
5.3046-5.46030.24761590.21113314347397
5.4603-5.63610.28961520.21593291344397
5.6361-5.83690.27991830.21743265344896
5.8369-6.06990.28391840.21763290347496
6.0699-6.34510.26121540.20483301345596
6.3451-6.67810.25011630.19443303346696
6.6781-7.09440.24061610.19823306346796
7.0944-7.63860.2351880.17893282347096
7.6386-8.40090.19611700.17553307347796
8.4009-9.60170.19131890.15723294348395
9.6017-12.04190.16311590.1673301346094
12.0419-39.94330.25221930.25363360355393

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