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

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Basic information

Entry
Database: PDB / ID: 4llg
TitleCrystal Structure Analysis of the E.coli holoenzyme/Gp2 complex
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • Bacterial RNA polymerase inhibitor
  • RNA polymerase sigma factor RpoD
KeywordsTRANSFERASE
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 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 / 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 / Resolution: 3.7936 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 9, 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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)894,08820
Polymers893,77714
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
M: Bacterial RNA polymerase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,04410
Polymers446,8897
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40320 Å2
ΔGint-208 kcal/mol
Surface area166360 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)447,04410
Polymers446,8897
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40320 Å2
ΔGint-204 kcal/mol
Surface area164120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.510, 205.038, 308.797
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 or (chain D and resseq 1152: 1213) or (chain F and resseq 1:56)
215chain N or (chain J and resseq 1152: 1213) or (chain L and resseq 1:56)
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 M or (chain D and resseq 1152: 1213) or (chain F and resseq 1:56)M15 - 64
1215chain M or (chain D and resseq 1152: 1213) or (chain F and resseq 1:56)D1152 - 1213
1315chain M or (chain D and resseq 1152: 1213) or (chain F and resseq 1:56)F1 - 56
2115chain N or (chain J and resseq 1152: 1213) or (chain L and resseq 1:56)N15 - 62
2215chain N or (chain J and resseq 1152: 1213) or (chain L and resseq 1:56)J1152 - 1213
2315chain N or (chain J and resseq 1152: 1213) or (chain L and resseq 1:56)L1 - 56
1116chain D and resseq 948:1022D948 - 1022
2116chain J and resseq 948:1022J948 - 1022
1117chain D and resseq 1023:1126D0
2117chain J and resseq 1023:1126J0

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

NCS oper:
IDCodeMatrixVector
1given(-0.416359, 0.001698, -0.909199), (-0.048601, -0.99861, 0.020392), (-0.907901, 0.052678, 0.415862)-68.007698, -219.856003, -38.634701
2given(-0.472648, 0.053082, -0.879651), (-0.087865, -0.996049, -0.012894), (-0.87686, 0.071196, 0.475445)-63.053299, -225.126007, -29.030899
3given(-0.346659, 0.055389, -0.936355), (-0.076915, -0.996572, -0.030476), (-0.934832, 0.061455, 0.349731)-58.2845, -225.682007, -44.9482
4given(-0.318037, 0.091911, -0.943613), (-0.101453, -0.992874, -0.062515), (-0.942635, 0.07585, 0.325095)-52.985901, -229.692993, -46.008202
5given(-0.416723, 0.002168, -0.909031), (-0.051253, -0.998462, 0.021114), (-0.907587, 0.055389, 0.416194)-68.158501, -219.932007, -38.109798
6given(-0.432781, -0.006667, -0.901474), (-0.028792, -0.99936, 0.021213), (-0.901039, 0.035136, 0.432312)-70.027397, -218.399002, -40.0611
7given(-0.395945, 0.014349, -0.918162), (-0.056033, -0.998392, 0.008561), (-0.916563, 0.054837, 0.396112)-64.811699, -221.085007, -39.932301
8given(-0.423085, 0.010457, -0.90603), (-0.040441, -0.999155, 0.007353), (-0.905187, 0.039752, 0.42315)-66.7043, -220.207001, -39.959
9given(-0.440877, 0.037761, -0.896773), (0.043112, -0.997071, -0.063179), (-0.896531, -0.066516, 0.437958)-61.720299, -224.438995, -57.509102
10given(-0.42215, -0.006585, -0.906502), (-0.029622, -0.999339, 0.021054), (-0.906042, 0.035741, 0.421676)-69.583199, -218.906998, -40.7131
11given(-0.421691, -0.001334, -0.906739), (-0.037806, -0.999103, 0.019053), (-0.905951, 0.042315, 0.421262)-68.757698, -218.899994, -39.734402
12given(-0.420215, 0.015842, -0.907286), (-0.049547, -0.998757, 0.005509), (-0.906071, 0.047269, 0.420477)-66.234802, -220.509003, -39.0504
13given(-0.404012, -0.014907, -0.914632), (-0.03229, -0.999012, 0.030546), (-0.914184, 0.041874, 0.403131)-69.0439, -218.126007, -41.018902
14given(-0.385083, -0.054357, -0.92128), (-0.035981, -0.996621, 0.073841), (-0.92218, 0.061584, 0.381826)-71.6875, -217.621002, -39.875301
15given(-0.416954, 0.000408, -0.908927), (-0.049863, -0.998504, 0.022425), (-0.907559, 0.054672, 0.416351)-68.124802, -219.759003, -38.4011
16given(-0.43358, -0.025016, -0.900768), (-0.03448, -0.998422, 0.044324), (-0.900455, 0.050276, 0.432033)-70.856003, -217.699997, -37.770699
17given(-0.42966, -0.029485, -0.902509), (-0.031059, -0.998393, 0.047403), (-0.902457, 0.048398, 0.428053)-71.165703, -217.313995, -38.278999

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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 / 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

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Protein , 2 types, 4 molecules FLMN

#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
#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: 6

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.96 %
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: Jun 12, 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: 3.7936→45.21 Å / Num. obs: 116763 / % possible obs: 99.9 % / Redundancy: 23.4 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
3.7936-3.9413.1198.9
3.94-4.0922.61100
4.09-4.2823.81100
4.28-4.524.511000.752
4.5-4.7924.911000.586
4.79-5.1625.311000.487
5.16-5.6725.511000.415
5.67-6.4925.611000.305
6.49-8.1725.211000.136
8.17-4523.611000.05

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7936→45.21 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.55 / σ(F): 1.35 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 5811 5.01 %
Rwork0.243 --
obs0.245 115875 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.72 Å2
Refinement stepCycle: LAST / Resolution: 3.7936→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59141 0 6 0 59147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00460052
X-RAY DIFFRACTIONf_angle_d0.82681086
X-RAY DIFFRACTIONf_dihedral_angle_d16.27223073
X-RAY DIFFRACTIONf_chiral_restr0.0599264
X-RAY DIFFRACTIONf_plane_restr0.00410625
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C11014X-RAY DIFFRACTIONPOSITIONAL0.026
12I11014X-RAY DIFFRACTIONPOSITIONAL0.026
21C1310X-RAY DIFFRACTIONPOSITIONAL0.076
22I1310X-RAY DIFFRACTIONPOSITIONAL0.076
31C1470X-RAY DIFFRACTIONPOSITIONAL0.011
32I1470X-RAY DIFFRACTIONPOSITIONAL0.011
41C912X-RAY DIFFRACTIONPOSITIONAL0.008
42I912X-RAY DIFFRACTIONPOSITIONAL0.008
51C549X-RAY DIFFRACTIONPOSITIONAL0.01
52I549X-RAY DIFFRACTIONPOSITIONAL0.01
61C1414X-RAY DIFFRACTIONPOSITIONAL0.014
62I1414X-RAY DIFFRACTIONPOSITIONAL0.014
71C148X-RAY DIFFRACTIONPOSITIONAL0.014
72I148X-RAY DIFFRACTIONPOSITIONAL0.014
81C3954X-RAY DIFFRACTIONPOSITIONAL0.017
82I3954X-RAY DIFFRACTIONPOSITIONAL0.017
91F1626X-RAY DIFFRACTIONPOSITIONAL0.016
92L1626X-RAY DIFFRACTIONPOSITIONAL0.016
101F836X-RAY DIFFRACTIONPOSITIONAL0.024
102L836X-RAY DIFFRACTIONPOSITIONAL0.024
111A762X-RAY DIFFRACTIONPOSITIONAL0.005
112G762X-RAY DIFFRACTIONPOSITIONAL0.005
121A963X-RAY DIFFRACTIONPOSITIONAL0.004
122G963X-RAY DIFFRACTIONPOSITIONAL0.004
131B762X-RAY DIFFRACTIONPOSITIONAL0.016
132H762X-RAY DIFFRACTIONPOSITIONAL0.016
141B855X-RAY DIFFRACTIONPOSITIONAL0.016
142H855X-RAY DIFFRACTIONPOSITIONAL0.016
151M1209X-RAY DIFFRACTIONPOSITIONAL0.041
152N1209X-RAY DIFFRACTIONPOSITIONAL0.041
161D562X-RAY DIFFRACTIONPOSITIONAL0.017
162J562X-RAY DIFFRACTIONPOSITIONAL0.017
171D778X-RAY DIFFRACTIONPOSITIONAL0.002
172J778X-RAY DIFFRACTIONPOSITIONAL0.002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7936-3.83670.37231260.33442185X-RAY DIFFRACTION60
3.8367-3.88180.34671800.32863324X-RAY DIFFRACTION89
3.8818-3.92910.37241850.30443622X-RAY DIFFRACTION98
3.9291-3.97880.38191990.30793634X-RAY DIFFRACTION99
3.9788-4.03110.36451850.3053724X-RAY DIFFRACTION100
4.0311-4.08630.36211920.29623681X-RAY DIFFRACTION100
4.0863-4.14470.36051940.29263681X-RAY DIFFRACTION100
4.1447-4.20650.32742160.27893698X-RAY DIFFRACTION100
4.2065-4.27220.33721970.27433725X-RAY DIFFRACTION100
4.2722-4.34220.29582030.27263668X-RAY DIFFRACTION100
4.3422-4.4170.3122100.2683680X-RAY DIFFRACTION100
4.417-4.49720.33071860.26023719X-RAY DIFFRACTION100
4.4972-4.58360.30131920.24623737X-RAY DIFFRACTION100
4.5836-4.67710.28712120.24973671X-RAY DIFFRACTION100
4.6771-4.77870.29281910.24913727X-RAY DIFFRACTION100
4.7787-4.88970.30331910.24353730X-RAY DIFFRACTION100
4.8897-5.01190.25851850.2473731X-RAY DIFFRACTION100
5.0119-5.14720.28362080.2483709X-RAY DIFFRACTION100
5.1472-5.29840.32941960.24373714X-RAY DIFFRACTION100
5.2984-5.46920.28051830.23983751X-RAY DIFFRACTION100
5.4692-5.66430.30221840.24193747X-RAY DIFFRACTION100
5.6643-5.89060.28042120.24683733X-RAY DIFFRACTION100
5.8906-6.15810.33011890.25543737X-RAY DIFFRACTION100
6.1581-6.48190.29471820.23713792X-RAY DIFFRACTION100
6.4819-6.88660.27931830.24383768X-RAY DIFFRACTION100
6.8866-7.41620.25912100.22533768X-RAY DIFFRACTION100
7.4162-8.15860.26021940.21443801X-RAY DIFFRACTION100
8.1586-9.33020.22692110.18733798X-RAY DIFFRACTION100
9.3302-11.7210.19861940.17933836X-RAY DIFFRACTION100
11.721-45.20920.25482210.25643973X-RAY DIFFRACTION100

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