[English] 日本語
Yorodumi
- PDB-7wsx: Class III hybrid cluster protein (HCP) C67Y variant from Methanot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wsx
TitleClass III hybrid cluster protein (HCP) C67Y variant from Methanothermobacter marburgensis
ComponentsHydroxylamine reductase
KeywordsOXIDOREDUCTASE / Hybrid cluster / Iron-sulfur cluster / enzyme / reductase / METAL BINDING PROTEIN
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / 4 iron, 4 sulfur cluster binding / iron ion binding / cytoplasm
Similarity search - Function
Hydroxylamine reductase / Prismane, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Rubredoxin domain / Rubredoxin / Prismane-like superfamily / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
FE-S-O HYBRID CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFujishiro, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
Japan Society for the Promotion of Science (JSPS)22K05137 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases.
Authors: Fujishiro, T. / Takaoka, K.
History
DepositionFeb 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydroxylamine reductase
B: Hydroxylamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7304
Polymers113,0592
Non-polymers6712
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-70 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.930, 70.560, 106.340
Angle α, β, γ (deg.)90.000, 106.850, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 89 through 491 or resid 601))
d_2ens_1(chain "B" and (resid 89 through 491 or resid 601))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAGLUGLUAA89 - 49189 - 491
d_12FS2FS2FS2FS2AC601
d_21ALAALAGLUGLUBB89 - 49189 - 491
d_22FS2FS2FS2FS2BD601

-
Components

#1: Protein Hydroxylamine reductase / Hybrid-cluster protein / HCP / Prismane protein


Mass: 56529.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter marburgensis (archaea)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: D9PYV4, hydroxylamine reductase
#2: Chemical ChemComp-FS2 / FE-S-O HYBRID CLUSTER


Mass: 335.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Ammonium acetate, 0.05 M HEPES-Na, 0.02 M MgCl2, 5% (w/v) PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→47.29 Å / Num. obs: 18596 / % possible obs: 99.6 % / Redundancy: 8.122 % / Biso Wilson estimate: 81.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.131 / Χ2: 0.989 / Net I/σ(I): 11.5 / Num. measured all: 151031 / Scaling rejects: 246
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.18.7120.9921.9717250.7461.05498.9
3.1-3.28.6330.7582.7715100.860.80699.7
3.2-3.38.3370.6783.2513360.860.72399.6
3.3-3.48.2440.5124.3311820.9220.54699.2
3.4-3.57.7340.4175.310380.9480.447100
3.5-48.0560.2189.3138880.9840.23399.5
4-58.0710.10816.9838270.9950.11599.9
5-68.0410.09219.2517010.9940.09999.6
6-107.7850.06823.3118590.9970.07399.6
10-47.296.9770.06326.35300.9960.06898

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W9M

1w9m


Resolution: 3→47.29 Å / SU ML: 0.4963 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 929 5 %RANDOM
Rwork0.2102 17652 --
obs0.2125 18581 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.17 Å2
Refinement stepCycle: LAST / Resolution: 3→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 18 2 6316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00366452
X-RAY DIFFRACTIONf_angle_d0.84598770
X-RAY DIFFRACTIONf_chiral_restr0.0523991
X-RAY DIFFRACTIONf_plane_restr0.00551127
X-RAY DIFFRACTIONf_dihedral_angle_d16.12912376
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.74632314955 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.3781310.29052493X-RAY DIFFRACTION99.09
3.16-3.360.29371300.26872479X-RAY DIFFRACTION98.98
3.36-3.620.30411320.25152512X-RAY DIFFRACTION99.74
3.62-3.980.30711330.21372513X-RAY DIFFRACTION99.85
3.98-4.550.24931330.18622530X-RAY DIFFRACTION100
4.55-5.740.20851330.18722529X-RAY DIFFRACTION99.81
5.74-47.290.22981370.19822596X-RAY DIFFRACTION99.56
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)
10.186383529292-0.0779416604128-0.006742260508090.04674266935760.2198059467670.1070668668750.00686114460837-0.6699734642430.0904540160634-0.1191342889720.04967471642470.0200382308573-0.1285881044540.0314548769368.2674083921E-90.4385097116310.002376493643590.02592321098260.50733369921-0.01293329590860.515860057621-39.9268627983-4.5961907651126.7670118387
20.4481033510340.329015695236-0.1574806349690.40979047505-0.6462122172590.228760087012-0.1107433452960.1122615214310.070206240311-0.09682310062350.1018424947440.100338372065-0.09348596254990.181464383078-1.27302890109E-90.6081392783610.014306792477-0.05483453834930.15918611435-0.03257305609370.573490009926-34.89043623477.652404011621.6490398975
30.2176443306660.181546187530.3414721501940.3373725444880.2061496657240.160380128899-0.0416581274533-0.02961212320790.00437166807931-0.1532542229980.05592030776370.0550549120735-0.07359473201870.03101476644117.83044351505E-90.5457139798910.0568933480824-0.05024148137850.2912543859310.04271163808640.833328324766-58.1049408393-1.069029764248.52954452793
4-0.05149175995270.04971629669890.02736675696330.0451118768685-0.1001770811890.1007656621740.0249616439355-0.259532044773-0.397568801504-0.0770184308146-0.04926345066060.2384482791690.0473006148196-0.01492752402346.53142505276E-80.4815390612610.02358674331430.02092924737270.4563083728650.1355155205170.909851162356-55.8928908894-14.831065469716.6979333597
50.346593613550.169342303893-0.00653891000019-0.00135073413546-0.01898270261320.06626446732070.108284932257-0.5313744136230.113513990352-0.376245615795-0.1721623177930.336599150598-0.1593308496580.2773790518664.23824269812E-90.60105250405-0.003920609011540.06021285656510.691145788898-0.1213037086080.481185508345-25.3875796236-4.7962122067129.248637689
6-0.05244296661350.4400566438230.01530431648-0.111328542107-0.2636040581440.347048939743-0.0710474473874-0.418016117179-0.135186277954-0.164617510031-0.2447252831470.6745871189390.03022937901610.453970277082-1.82308013564E-90.535520720478-0.05256543005240.04400963517751.42283966330.02400912369270.294921757078-30.3388125953-18.51926622153.418959873
70.114661015328-0.4433865546430.1611042043660.335104881527-0.08499672452970.238569757650.225928785339-0.244172542004-0.04061075019390.0145798315876-0.1684496031180.08925975058160.009357675380610.1906336861078.81481807081E-90.5003502750660.005891185222530.02097410977041.445332772460.07674782023330.463549846625-6.24628718239-16.365646295143.639846733
80.00405279421818-0.0378619743021-0.01969970108-0.0466523338596-0.06387821581610.1683186897290.23159817982-0.24999304773-0.158552946889-0.880360917114-0.104379465005-0.3103434392930.102843439948-0.1196545936871.55809436555E-80.5413424097250.175152000548-0.07167928922221.062395585120.1149995064460.414323715011-9.44985650819-19.415726059328.2592292998
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 88 through 170 )AA88 - 1701 - 83
22chain 'A' and (resid 171 through 325 )AA171 - 32584 - 238
33chain 'A' and (resid 326 through 437 )AA326 - 437239 - 350
44chain 'A' and (resid 438 through 491 )AA438 - 491351 - 404
55chain 'B' and (resid 89 through 170 )BC89 - 1701 - 82
66chain 'B' and (resid 171 through 325 )BC171 - 32583 - 237
77chain 'B' and (resid 326 through 433 )BC326 - 433238 - 345
88chain 'B' and (resid 434 through 492 )BC434 - 492346 - 404

+
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://pdbjlvh1.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