[English] 日本語
Yorodumi
- PDB-1gnt: Hybrid Cluster Protein from Desulfovibrio vulgaris. X-ray structu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gnt
TitleHybrid Cluster Protein from Desulfovibrio vulgaris. X-ray structure at 1.25A resolution using synchrotron radiation.
ComponentsHYBRID CLUSTER PROTEIN
KeywordsOXIDOREDUCTASE / HYBRID CLUSTER PROTEIN / AEROBIC DESULFOVIBRIO VULGARIS
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #20 / Hydroxylamine reductase / Prismane, alpha-bundle / Rossmann fold - #2030 / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #20 / Hydroxylamine reductase / Prismane, alpha-bundle / Rossmann fold - #2030 / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR/OXYGEN HYBRID CLUSTER / IRON/SULFUR CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMacedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / Legall, J. / Bailey, S. / Garner, D.C. ...Macedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / Legall, J. / Bailey, S. / Garner, D.C. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2002
Title: Hybrid cluster proteins (HCPs) from Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio vulgaris (Hildenborough): X-ray structures at 1.25 A resolution using synchrotron radiation.
Authors: Macedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / LeGall, J. / Bailey, S. / Garner, D.C. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P.
History
DepositionOct 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 6, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.4Dec 23, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value ..._pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_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_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 1.5Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYBRID CLUSTER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7623
Polymers60,0431
Non-polymers7192
Water18,2851015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.810, 64.530, 151.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HYBRID CLUSTER PROTEIN / HCP


Mass: 60042.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S-3O] PERSULPHIDE BOND BETWEEN S7 (HYBRID CLUSTER) AND S OF CYS406
Source: (gene. exp.) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH NCIMB8303 / Plasmid: PJSP104 / Production host: DESULFOVIBRIO VULGARIS (bacteria) / Strain (production host): HILDENBOROUGH NCIMB8303 / References: UniProt: P31101
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FSO / IRON/SULFUR/OXYGEN HYBRID CLUSTER


Mass: 367.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4O3S3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1015 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 25-30% PEG 8000 0.1M MES PH 5.9, 0.2M MAGNESIUM ACETATE, T=277K
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MMES1reservoirpH5.9
20.2 Mmagnesium acetate1reservoir
325-30 %PEG80001reservoir
412 mg/mlprotein1drop
55 mMTris-HCl1droppH8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1999 / Details: PLATINUM COATED FUSED QUARTZ MIRROR
RadiationMonochromator: SI(111) BENT TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.25→19.92 Å / Num. obs: 163543 / % possible obs: 94.6 % / Redundancy: 2.4 % / Rsym value: 0.063 / Net I/σ(I): 6.2
Reflection shellResolution: 1.25→1.34 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.331 / % possible all: 86.4
Reflection
*PLUS
Num. measured all: 400513 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 86.4 % / Rmerge(I) obs: 0.331

-
Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB FROM ENTRY 1E2U
Resolution: 1.25→19.92 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.978 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.173 8216 5 %RANDOM
Rwork0.157 ---
obs0.158 155271 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 1.25→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 18 1015 5250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224346
X-RAY DIFFRACTIONr_bond_other_d0.0010.024013
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.4671.9695891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.16839372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02822
X-RAY DIFFRACTIONr_nbd_refined0.2310.3942
X-RAY DIFFRACTIONr_nbd_other0.180.33704
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.3390.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5687
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.567
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6931.52748
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21724421
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89531598
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0644.51470
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 548
Rwork0.284 10111
Software
*PLUS
Name: REFMAC / Version: '5.0.36 18/01/2001' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.157 / Rfactor Rfree: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.462
X-RAY DIFFRACTIONp_plane_restr0.006
X-RAY DIFFRACTIONp_chiral_restr0.105
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / Num. reflection Rfree: 548 / Rfactor Rwork: 0.284 / Num. reflection obs: 10111 / Rfactor obs: 0.284

+
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