[English] 日本語
Yorodumi
- PDB-6pfz: Structure of a NAD-Dependent Persulfide Reductase from A. fulgidus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pfz
TitleStructure of a NAD-Dependent Persulfide Reductase from A. fulgidus
ComponentsNADH oxidase (NoxA-3)
KeywordsFLAVOPROTEIN / NADH-dependent Reductase / persulfide reductase / disulfide reductase / polysulfide reductase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...: / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / NADH oxidase (NoxA-3)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.10003870577 Å
AuthorsSazinsky, M.H. / Shabdar, S. / Garcia-Constineiras, A. / Crane III, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1518306 United States
CitationJournal: Archaea / Year: 2021
Title: Structural and Kinetic Characterization of Hyperthermophilic NADH-Dependent Persulfide Reductase from Archaeoglobus fulgidus .
Authors: Shabdar, S. / Anaclet, B. / Castineiras, A.G. / Desir, N. / Choe, N. / Crane 3rd, E.J. / Sazinsky, M.H.
History
DepositionJun 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _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_conn.ptnr2_label_seq_id
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: NADH oxidase (NoxA-3)
A: NADH oxidase (NoxA-3)
B: NADH oxidase (NoxA-3)
C: NADH oxidase (NoxA-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,38916
Polymers241,0164
Non-polymers6,37312
Water25214
1
D: NADH oxidase (NoxA-3)
C: NADH oxidase (NoxA-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6948
Polymers120,5082
Non-polymers3,1866
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-78 kcal/mol
Surface area38490 Å2
MethodPISA
2
A: NADH oxidase (NoxA-3)
B: NADH oxidase (NoxA-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6948
Polymers120,5082
Non-polymers3,1866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-81 kcal/mol
Surface area38400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.976, 100.355, 136.196
Angle α, β, γ (deg.)90.000, 91.894, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resseq 1:4 or (resid 5 and (name...AB1 - 331 - 33
12TYRTYRGLUGLU(chain A and (resseq 1:4 or (resid 5 and (name...AB36 - 6036 - 60
13ARGARGVALVAL(chain A and (resseq 1:4 or (resid 5 and (name...AB67 - 9967 - 99
14ASNASNILEILE(chain A and (resseq 1:4 or (resid 5 and (name...AB101 - 128101 - 128
15ALAALAGLUGLU(chain A and (resseq 1:4 or (resid 5 and (name...AB130 - 143130 - 143
16ILEILEGLYGLY(chain A and (resseq 1:4 or (resid 5 and (name...AB145 - 152145 - 152
17LYSLYSMETMET(chain A and (resseq 1:4 or (resid 5 and (name...AB155 - 177155 - 177
18VALVALASPASP(chain A and (resseq 1:4 or (resid 5 and (name...AB179 - 194179 - 194
19GLUGLUSERSER(chain A and (resseq 1:4 or (resid 5 and (name...AB196 - 223196 - 223
110ARGARGVALVAL(chain A and (resseq 1:4 or (resid 5 and (name...AB229 - 231229 - 231
111ASNASNILEILE(chain A and (resseq 1:4 or (resid 5 and (name...AB234 - 249234 - 249
112PROPROGLUGLU(chain A and (resseq 1:4 or (resid 5 and (name...AB251 - 257251 - 257
113ALAALAILEILE(chain A and (resseq 1:4 or (resid 5 and (name...AB259 - 263259 - 263
114THRTHRGLYGLY(chain A and (resseq 1:4 or (resid 5 and (name...AB266 - 321266 - 321
115ALAALATRPTRP(chain A and (resseq 1:4 or (resid 5 and (name...AB324 - 390324 - 390
116VALVALPHEPHE(chain A and (resseq 1:4 or (resid 5 and (name...AB392 - 462392 - 462
117ILEILESERSER(chain A and (resseq 1:4 or (resid 5 and (name...AB473 - 480473 - 480
118GLUGLUGLUGLU(chain A and (resseq 1:4 or (resid 5 and (name...AB483483
119LYSLYSARGARG(chain A and (resseq 1:4 or (resid 5 and (name...AB493 - 503493 - 503
120ARGARGLEULEU(chain A and (resseq 1:4 or (resid 5 and (name...AB505 - 506505 - 506
121GLUGLUPROPRO(chain A and (resseq 1:4 or (resid 5 and (name...AB508 - 510508 - 510
122LYSLYSLEULEU(chain A and (resseq 1:4 or (resid 5 and (name...AB513 - 532513 - 532
123ALAALAPHEPHE(chain A and (resseq 1:4 or (resid 5 and (name...AB535 - 537535 - 537
124LYSLYSPHEPHE(chain A and (resseq 1:4 or (resid 5 and (name...AB539 - 551539 - 551
125FADFADFADFAD(chain A and (resseq 1:4 or (resid 5 and (name...AG901
21METMETALAALA(chain B and (resseq 1:4 or (resid 5 and (name...BC1 - 331 - 33
22TYRTYRGLUGLU(chain B and (resseq 1:4 or (resid 5 and (name...BC36 - 6036 - 60
23ARGARGVALVAL(chain B and (resseq 1:4 or (resid 5 and (name...BC67 - 9967 - 99
24ASNASNILEILE(chain B and (resseq 1:4 or (resid 5 and (name...BC101 - 128101 - 128
25ALAALAGLUGLU(chain B and (resseq 1:4 or (resid 5 and (name...BC130 - 143130 - 143
26ILEILEGLYGLY(chain B and (resseq 1:4 or (resid 5 and (name...BC145 - 152145 - 152
27LYSLYSMETMET(chain B and (resseq 1:4 or (resid 5 and (name...BC155 - 177155 - 177
28VALVALASPASP(chain B and (resseq 1:4 or (resid 5 and (name...BC179 - 194179 - 194
29GLUGLUSERSER(chain B and (resseq 1:4 or (resid 5 and (name...BC196 - 223196 - 223
210ARGARGVALVAL(chain B and (resseq 1:4 or (resid 5 and (name...BC229 - 231229 - 231
211ASNASNILEILE(chain B and (resseq 1:4 or (resid 5 and (name...BC234 - 249234 - 249
212PROPROGLUGLU(chain B and (resseq 1:4 or (resid 5 and (name...BC251 - 257251 - 257
213ALAALAILEILE(chain B and (resseq 1:4 or (resid 5 and (name...BC259 - 263259 - 263
214THRTHRGLYGLY(chain B and (resseq 1:4 or (resid 5 and (name...BC266 - 321266 - 321
215ALAALATRPTRP(chain B and (resseq 1:4 or (resid 5 and (name...BC324 - 390324 - 390
216VALVALPHEPHE(chain B and (resseq 1:4 or (resid 5 and (name...BC392 - 462392 - 462
217ILEILESERSER(chain B and (resseq 1:4 or (resid 5 and (name...BC473 - 480473 - 480
218GLUGLUGLUGLU(chain B and (resseq 1:4 or (resid 5 and (name...BC483483
219LYSLYSARGARG(chain B and (resseq 1:4 or (resid 5 and (name...BC493 - 503493 - 503
220ARGARGLEULEU(chain B and (resseq 1:4 or (resid 5 and (name...BC505 - 506505 - 506
221GLUGLUPROPRO(chain B and (resseq 1:4 or (resid 5 and (name...BC508 - 510508 - 510
222LYSLYSLEULEU(chain B and (resseq 1:4 or (resid 5 and (name...BC513 - 532513 - 532
223ALAALAPHEPHE(chain B and (resseq 1:4 or (resid 5 and (name...BC535 - 537535 - 537
224LYSLYSPHEPHE(chain B and (resseq 1:4 or (resid 5 and (name...BC539 - 551539 - 551
225FADFADFADFAD(chain B and (resseq 1:4 or (resid 5 and (name...BJ901
31METMETALAALA(chain C and (resseq 1:4 or (resid 5 and (name...CD1 - 331 - 33
32TYRTYRGLUGLU(chain C and (resseq 1:4 or (resid 5 and (name...CD36 - 6036 - 60
33ARGARGVALVAL(chain C and (resseq 1:4 or (resid 5 and (name...CD67 - 9967 - 99
34ASNASNILEILE(chain C and (resseq 1:4 or (resid 5 and (name...CD101 - 128101 - 128
35ALAALAGLUGLU(chain C and (resseq 1:4 or (resid 5 and (name...CD130 - 143130 - 143
36ILEILEGLYGLY(chain C and (resseq 1:4 or (resid 5 and (name...CD145 - 152145 - 152
37LYSLYSMETMET(chain C and (resseq 1:4 or (resid 5 and (name...CD155 - 177155 - 177
38VALVALASPASP(chain C and (resseq 1:4 or (resid 5 and (name...CD179 - 194179 - 194
39GLUGLUSERSER(chain C and (resseq 1:4 or (resid 5 and (name...CD196 - 223196 - 223
310ARGARGVALVAL(chain C and (resseq 1:4 or (resid 5 and (name...CD229 - 231229 - 231
311ASNASNILEILE(chain C and (resseq 1:4 or (resid 5 and (name...CD234 - 249234 - 249
312PROPROGLUGLU(chain C and (resseq 1:4 or (resid 5 and (name...CD251 - 257251 - 257
313ALAALAILEILE(chain C and (resseq 1:4 or (resid 5 and (name...CD259 - 263259 - 263
314THRTHRGLYGLY(chain C and (resseq 1:4 or (resid 5 and (name...CD266 - 321266 - 321
315ALAALATRPTRP(chain C and (resseq 1:4 or (resid 5 and (name...CD324 - 390324 - 390
316VALVALPHEPHE(chain C and (resseq 1:4 or (resid 5 and (name...CD392 - 462392 - 462
317ILEILESERSER(chain C and (resseq 1:4 or (resid 5 and (name...CD473 - 480473 - 480
318GLUGLUGLUGLU(chain C and (resseq 1:4 or (resid 5 and (name...CD483483
319LYSLYSARGARG(chain C and (resseq 1:4 or (resid 5 and (name...CD493 - 503493 - 503
320ARGARGLEULEU(chain C and (resseq 1:4 or (resid 5 and (name...CD505 - 506505 - 506
321GLUGLUPROPRO(chain C and (resseq 1:4 or (resid 5 and (name...CD508 - 510508 - 510
322LYSLYSLEULEU(chain C and (resseq 1:4 or (resid 5 and (name...CD513 - 532513 - 532
323ALAALAPHEPHE(chain C and (resseq 1:4 or (resid 5 and (name...CD535 - 537535 - 537
324LYSLYSPHEPHE(chain C and (resseq 1:4 or (resid 5 and (name...CD539 - 551539 - 551
325FADFADFADFAD(chain C and (resseq 1:4 or (resid 5 and (name...CM901
41METMETALAALA(chain D and (resseq 1:4 or (resid 5 and (name...DA1 - 331 - 33
42TYRTYRGLUGLU(chain D and (resseq 1:4 or (resid 5 and (name...DA36 - 6036 - 60
43ARGARGVALVAL(chain D and (resseq 1:4 or (resid 5 and (name...DA67 - 9967 - 99
44ASNASNILEILE(chain D and (resseq 1:4 or (resid 5 and (name...DA101 - 128101 - 128
45ALAALAGLUGLU(chain D and (resseq 1:4 or (resid 5 and (name...DA130 - 143130 - 143
46ILEILEGLYGLY(chain D and (resseq 1:4 or (resid 5 and (name...DA145 - 152145 - 152
47LYSLYSMETMET(chain D and (resseq 1:4 or (resid 5 and (name...DA155 - 177155 - 177
48VALVALASPASP(chain D and (resseq 1:4 or (resid 5 and (name...DA179 - 194179 - 194
49GLUGLUSERSER(chain D and (resseq 1:4 or (resid 5 and (name...DA196 - 223196 - 223
410ARGARGVALVAL(chain D and (resseq 1:4 or (resid 5 and (name...DA229 - 231229 - 231
411ASNASNILEILE(chain D and (resseq 1:4 or (resid 5 and (name...DA234 - 249234 - 249
412PROPROGLUGLU(chain D and (resseq 1:4 or (resid 5 and (name...DA251 - 257251 - 257
413ALAALAILEILE(chain D and (resseq 1:4 or (resid 5 and (name...DA259 - 263259 - 263
414THRTHRGLYGLY(chain D and (resseq 1:4 or (resid 5 and (name...DA266 - 321266 - 321
415ALAALATRPTRP(chain D and (resseq 1:4 or (resid 5 and (name...DA324 - 390324 - 390
416VALVALPHEPHE(chain D and (resseq 1:4 or (resid 5 and (name...DA392 - 462392 - 462
417ILEILESERSER(chain D and (resseq 1:4 or (resid 5 and (name...DA473 - 480473 - 480
418GLUGLUGLUGLU(chain D and (resseq 1:4 or (resid 5 and (name...DA483483
419LYSLYSARGARG(chain D and (resseq 1:4 or (resid 5 and (name...DA493 - 503493 - 503
420ARGARGLEULEU(chain D and (resseq 1:4 or (resid 5 and (name...DA505 - 506505 - 506
421GLUGLUPROPRO(chain D and (resseq 1:4 or (resid 5 and (name...DA508 - 510508 - 510
422LYSLYSLEULEU(chain D and (resseq 1:4 or (resid 5 and (name...DA513 - 532513 - 532
423ALAALAPHEPHE(chain D and (resseq 1:4 or (resid 5 and (name...DA535 - 537535 - 537
424LYSLYSPHEPHE(chain D and (resseq 1:4 or (resid 5 and (name...DA539 - 551539 - 551
425FADFADFADFAD(chain D and (resseq 1:4 or (resid 5 and (name...DE901

-
Components

#1: Protein
NADH oxidase (NoxA-3)


Mass: 60254.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_0400 / Production host: Escherichia coli (E. coli) / References: UniProt: O29847
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100-200 mM calcium acetate, 15-20% PEG 3350 (w/w), and 1 mM DTT

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2016
Details: Cryogenically-cooled single crystal Si(220) side bounce monochromator.
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 80127 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 58.5513273334 Å2 / Rsym value: 0.119 / Net I/σ(I): 10.3
Reflection shellResolution: 3.1→3.27 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6083 / Rsym value: 0.54

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FX9

4fx9


Resolution: 3.10003870577→39.4818037712 Å / SU ML: 0.313808297468 / Cross valid method: FREE R-VALUE / σ(F): 1.06887880485 / Phase error: 22.6307325214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228746674435 2782 3.48272408613 %
Rwork0.202274311858 77098 -
obs0.203188436559 79880 97.8645724857 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.5125936023 Å2
Refinement stepCycle: LAST / Resolution: 3.10003870577→39.4818037712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16658 0 4 14 16676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023963099815616914
X-RAY DIFFRACTIONf_angle_d1.9872641866922984
X-RAY DIFFRACTIONf_chiral_restr0.2927769680122680
X-RAY DIFFRACTIONf_plane_restr0.01196898498292920
X-RAY DIFFRACTIONf_dihedral_angle_d24.69297800966121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.15350.2959278307361470.2982326729213977X-RAY DIFFRACTION99.0869774147
3.1535-3.21080.333042308051340.2882649407043846X-RAY DIFFRACTION98.8574267263
3.2108-3.27250.2949866838241580.2746348808633886X-RAY DIFFRACTION98.802834107
3.2725-3.33930.2880127162571300.2590795845153904X-RAY DIFFRACTION98.7999020328
3.3393-3.41180.2845786049961280.2476542254993935X-RAY DIFFRACTION98.8324008757
3.4118-3.49120.2385869692851520.2476925071273719X-RAY DIFFRACTION96.1500248385
3.4912-3.57840.2674210577791310.2252106128943951X-RAY DIFFRACTION99.0295972829
3.5784-3.67510.232854294951500.2170149195593782X-RAY DIFFRACTION96.3017389175
3.6751-3.78320.2488615699041210.2098828142483835X-RAY DIFFRACTION98.3834866949
3.7832-3.90520.2151505343021480.2062139379413807X-RAY DIFFRACTION96.3928832562
3.9052-4.04460.2133235546921450.19686968353889X-RAY DIFFRACTION98.3422720624
4.0446-4.20640.2299568635931380.1829323770653855X-RAY DIFFRACTION98.7144622991
4.2064-4.39760.226213960311350.1712775720063902X-RAY DIFFRACTION98.3434835566
4.3976-4.62910.1901348904241430.1658613587743800X-RAY DIFFRACTION98.0845771144
4.6291-4.91860.1922697184271410.1651495965123907X-RAY DIFFRACTION98.2285852948
4.9186-5.29760.2036412946111360.181102494483887X-RAY DIFFRACTION98.3859134263
5.2976-5.82920.2113637694391330.2040708597153875X-RAY DIFFRACTION98.2112227395
5.8292-6.66920.2117779374781330.1975623925313814X-RAY DIFFRACTION96.9778869779
6.6692-8.38920.2072762149761420.1746770648773825X-RAY DIFFRACTION97.2303921569
8.3892-39.4850.2148034710091370.180695679673702X-RAY DIFFRACTION94.2779960707
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)
11.92368640827-0.6162384357460.2035728111710.8530125808990.3198369817842.03689994473-0.0961450741247-0.04409766785290.149170767312-0.04224239087230.02480422110470.115968298826-0.201740040377-0.1834281089510.1076161267530.412555842754-0.03361392266340.04394190214220.342956392022-0.03866788193910.414284469425-32.1510048328.8673002943203.822341323
22.79528501480.6161443746950.8668181109731.534618078870.01294452395011.81093356624-0.02098885923990.249960538192-0.4118654601040.141953767666-0.1723767154850.5291667271490.43264496546-0.1241582054660.2700034913390.399344684756-0.04443608764570.09504446623130.342812990523-0.08959513043160.442053836423-26.332003974412.3535216679199.526462372
33.884694644961.44141547268-0.8701375035923.33005747081-1.114329245482.947349485950.0809573965809-0.302196957588-0.1979226300330.418163117642-0.07731581793230.02984905038240.1804529495780.05238161030180.04383477619920.3619252349120.03929371584330.03819228659370.2784998604370.008750906084570.281038255638-5.4080033910618.0493665082214.726030235
43.98674223211-0.494435591572-3.379493174212.663214444580.5532904422166.572648139740.194408000603-0.431355848967-0.4162188132730.166898849835-0.385457861434-0.08303998669760.1165494445460.186308665630.199123492180.3363274697760.0561263332035-0.03638801664180.4504583853760.01721637653620.410478625583-2.9116633982813.2861109401227.409505994
54.93323643529-0.245227313032-2.311475244171.246500030931.25141732521.790715526440.0114515621192-0.6736070702590.02610726898831.22887800769-0.2627820069160.0215394392566-0.0849414555406-0.1603646050460.1344618806640.726610083022-0.02883774380460.07229443844750.897833077793-0.100912728590.3646753696613.5813372275324.6415610308241.898718512
67.96185612401-1.14000973816-0.5709607204162.418757037721.753644653383.10219482422-0.60286838697-0.973658859708-0.4339709022780.8123864815790.254617641488-0.0162718930789-0.04420974810950.09095526194320.3575098764490.5529386259530.041006600179-0.05045635099350.7954425364360.03967954763410.4432906607740.8059753052318.2108144914234.53600616
70.002306691239410.129729735729-0.0298937182455-0.12385162234-0.1235126165111.307375121020.0901444497975-0.307255845943-0.1227596204670.4748868389360.172574691165-0.03720627852910.4353590934470.208297811746-0.02150628218280.399753596261-0.0302933001129-0.03719316098150.348218473924-0.01409798146540.4291280836812.8709138993-2.64997906454154.809418594
81.45459246363-0.235971471369-0.2239116506721.892219700221.241802752951.961871750360.03509786724760.1757431464380.0342208919282-0.110484319196-0.07090349659430.213945437915-0.0561237099561-0.22200318876-0.05610134411330.2144687034790.00348567003812-0.01674405448020.2956052003180.06329941490010.3100559814696.235630961-3.4135908801136.165223266
91.670635960010.20279748815-0.5924824974630.576238427656-0.4749675527050.807236152576-0.005283086546420.1899227293490.01293099690640.01744097554540.1132484611070.0656811021470.003764763549550.0004301675868160.04021967086410.2477707692720.00456984611066-0.03288528172030.2112610344190.0407480590250.22253274729229.14622901114.58052352746131.904556644
100.106966559059-0.5483010546721.34003569530.623495345252-1.326205284044.308270010080.1527995443641.059159516280.205301384849-0.2060390250820.04425515805710.243142913293-0.31432867216-0.1459919889160.3312832832180.3850983516150.03938892503560.02272029037560.571891803908-0.02555435217690.55942834241836.91357166593.773745268113.565366304
111.37746431502-0.0744479049907-0.5894870942290.8532966722380.6706526206652.29188087490.001222873509240.317911187237-0.0105062564453-0.136153139606-0.0565292994230.008097811534240.378088270269-0.3142666497180.03161362356310.3541685933440.02679961410140.02212236721450.570729564819-0.03835168509890.37759049197842.5180239132-5.79041524319105.223854214
120.636926736889-0.8106719391660.007317900983820.976056869985-1.115323787072.42510369787-0.07719365603740.257269953981-0.325477069248-0.4563878424250.0655117078453-0.1647002406630.504423795926-0.360073870449-0.0697196427540.394665498334-0.03558077207130.006133537930.3431823983640.002015791436380.34974349459260.4210510394-3.93758791751120.658159848
131.536914826910.291492156998-0.09290232155611.81341134255-1.262043008611.797823727350.032905378265-0.151419076138-0.264301250101-0.0418223360317-0.100780335551-0.2068068719080.1020567255620.231185795537-0.01945923510890.179863866928-0.03140530614380.02315846539020.173649617292-0.02637787918530.23745840521562.1164849557-1.16552490468139.842640599
142.11934424875-0.9291939767871.138901112830.2846520268880.02711623942342.441243806820.0625499146637-0.1947250158270.1878820108260.159883927985-0.0411805220612-0.10001609030.007241245722720.1172349481790.01521765492360.257780518318-0.008663525436430.05980925233920.1603335845120.006672711192180.25856025325436.54406728744.04787368356147.521352808
154.26747668959-1.026845965273.134762922823.10005108313-3.36539408146.716778293050.133786578452-0.575512818590.01067222976160.8058418060930.0471757435077-0.516203115278-0.1799059246550.4918410714230.06720112920890.340092196645-0.0211183640798-0.03984542129960.385983499993-0.04577441577060.32764071209934.94162298746.4935576497161.880123233
161.50932531118-0.1221645265520.9498963855170.888263501132-0.9220279600471.186252393090.18049805939-0.688118855583-0.1453820718140.430637656688-0.2443736972540.05909607269830.2047000246640.146083573991-0.1228391422260.3530942379930.02466485767080.07582212939760.5400334640890.04421239421610.3658253602128.3502461627-4.14809394751172.804487544
173.35995279269-2.17445611965-0.6712044186682.359411931610.5113541381080.6311438378210.680829923755-0.438238479706-0.321018217086-0.232542864856-0.292752209626-0.499029878259-0.05492429547050.4169302087940.121644456320.4470980291160.0139867207358-0.02517178172960.5243168543090.009370739436490.28551798253730.13352732082.19518475547166.436656136
180.4311612998480.109610869806-0.1434760664180.997309799034-1.014362961671.51494159034-0.0666507837473-0.3196556630570.2112264261780.1766016742950.0828727939822-0.0750796047588-0.1168947554020.104102396345-0.06089426711120.3792591336620.0567561663903-0.01755720250370.4412892369230.01621621896520.40113497452723.960278709125.3351393632215.792122518
191.91122689169-0.100850959516-0.3994800404671.71906309937-0.7253400655881.07962514732-0.008350587854520.1451467998340.0295905684288-0.136649693056-0.00319687041662-0.2043910001760.02997018644480.206881506788-0.0597315335090.3560069271860.02537261454950.0495444154630.287343423292-0.09565566002260.27470091662120.885241108424.1327740404197.639477023
202.010696225310.1192427060180.557586463590.6829276730450.02970157612580.690910627866-0.006066634649880.159330506394-0.124636035817-0.06801476049060.04392705795260.111825727765-0.01049285883550.084883157216-0.1536160103630.43597527262-0.02071526579350.05869736069260.316201214499-0.01982293016090.303793007565-1.1084734260119.4689755672197.682092028
210.1279909495580.374128535494-0.06988150616640.463661953367-0.01904196288650.7044101755340.08242397180260.4010657914830.4690473989740.0991587996192-0.291619359640.1167796243070.0730588813355-0.0271009561653-0.1192451055480.8808760724250.0180044920246-0.05536825004660.8464489916380.08708758124660.54161920151-10.482636654532.024678054172.655210404
220.0908748684644-0.1784864291960.1908128641230.113835690697-0.1587487158450.0555559761112-0.2362374516810.439507682505-0.1405680221890.526389396534-0.2290731937270.231914683287-0.06045063086060.08209582967887.65784837033E-80.442400554367-0.0216104976079-0.05928836295230.7753590989120.06135753298010.292149219163-10.016783576127.0259366961176.189609242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 253 )
2X-RAY DIFFRACTION2chain 'D' and (resid 254 through 340 )
3X-RAY DIFFRACTION3chain 'D' and (resid 341 through 439 )
4X-RAY DIFFRACTION4chain 'D' and (resid 440 through 472 )
5X-RAY DIFFRACTION5chain 'D' and (resid 473 through 513 )
6X-RAY DIFFRACTION6chain 'D' and (resid 514 through 551 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 76 )
8X-RAY DIFFRACTION8chain 'A' and (resid 77 through 284 )
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 439 )
10X-RAY DIFFRACTION10chain 'A' and (resid 440 through 472 )
11X-RAY DIFFRACTION11chain 'A' and (resid 473 through 551 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 340 )
14X-RAY DIFFRACTION14chain 'B' and (resid 341 through 439 )
15X-RAY DIFFRACTION15chain 'B' and (resid 440 through 473 )
16X-RAY DIFFRACTION16chain 'B' and (resid 474 through 522 )
17X-RAY DIFFRACTION17chain 'B' and (resid 523 through 551 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 175 )
19X-RAY DIFFRACTION19chain 'C' and (resid 176 through 304 )
20X-RAY DIFFRACTION20chain 'C' and (resid 305 through 452 )
21X-RAY DIFFRACTION21chain 'C' and (resid 453 through 513 )
22X-RAY DIFFRACTION22chain 'C' and (resid 514 through 551 )

+
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