[English] 日本語
Yorodumi
- PDB-7kom: High Resolution Crystal Structure of Putative Pterin Binding Prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kom
TitleHigh Resolution Crystal Structure of Putative Pterin Binding Protein PruR (VV2_1280) from Vibrio vulnificus CMCP6
ComponentsOxidored_molyb domain-containing protein
KeywordsPterin binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Pterin binding / pterin / UNKNOWN FUNCTION
Function / homologyOxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / FORMIC ACID / Oxidoreductase molybdopterin-binding domain-containing protein
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.99 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Control of biofilm formation by an Agrobacterium tumefaciens pterin-binding periplasmic protein conserved among diverse Proteobacteria.
Authors: Greenwich, J.L. / Eagan, J.L. / Feirer, N. / Boswinkle, K. / Minasov, G. / Shuvalova, L. / Inniss, N.L. / Raghavaiah, J. / Ghosh, A.K. / Satchell, K.J.F. / Allen, K.D. / Fuqua, C.
History
DepositionNov 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 11, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oxidored_molyb domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3264
Polymers16,2111
Non-polymers1153
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.046, 71.087, 106.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

21A-327-

HOH

31A-438-

HOH

41A-461-

HOH

-
Components

#1: Protein Oxidored_molyb domain-containing protein


Mass: 16210.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (strain CMCP6) (bacteria)
Strain: CMCP6 / Gene: VV2_1280 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: A0A3Q0L063
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Protein: 7.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (A7), 0.1M Citric acid (pH 3.5), 3.0M Sodium chloride. Cryo: 4.0M Formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2018 / Details: Be
RadiationMonochromator: Diamond (C111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 0.99→30 Å / Num. obs: 65367 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.03 / Rrim(I) all: 0.081 / Rsym value: 0.075 / Χ2: 2.854 / Net I/σ(I): 45.1
Reflection shellResolution: 0.99→1.01 Å / Redundancy: 6 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2840 / CC1/2: 0.821 / CC star: 0.95 / Rpim(I) all: 0.288 / Rrim(I) all: 0.74 / Rsym value: 0.679 / Χ2: 1.003 / % possible all: 82.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 0.99→26.6 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.55 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.141 3176 4.9 %RANDOM
Rwork0.1195 ---
obs0.1205 62187 93.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.57 Å2 / Biso mean: 9.117 Å2 / Biso min: 3.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 0.99→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 7 254 1359
Biso mean--19.26 20.72 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171314
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6592004
X-RAY DIFFRACTIONr_angle_other_deg1.3891.5743084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9265191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41722.62580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.82615238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3041510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021737
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02309
X-RAY DIFFRACTIONr_rigid_bond_restr9.19632759
LS refinement shellResolution: 0.99→1.016 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 201 -
Rwork0.26 4069 -
all-4270 -
obs--82.91 %
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)
10.73990.3396-0.21540.6736-0.07690.4673-0.0121-0.0011-0.02780.0236-0.0092-0.01660.0307-0.00390.02130.02130.0022-0.00560.0178-0.00090.00414.297218.403141.8908
20.9209-0.02310.62320.95770.68812.25480.046-0.0367-0.12710.09770.0088-0.01810.1967-0.0446-0.05470.0339-0.0068-0.00780.01930.01010.02511.50111.660442.7019
30.82430.0160.03720.25350.15350.1363-0.0120.01460.013-0.00450.0072-0.0044-0.00960.01070.00480.0233-0.0016-0.00260.01150.0010.001511.407422.845438.5822
44.5041-2.57653.18154.3649-2.10683.28790.1024-0.0237-0.2086-0.0175-0.0307-0.01310.1278-0.0049-0.07170.0223-0.00080.00260.01230.00550.02289.4198.635138.895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 62
2X-RAY DIFFRACTION2A63 - 90
3X-RAY DIFFRACTION3A91 - 145
4X-RAY DIFFRACTION4A146 - 152

+
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