[English] 日本語
Yorodumi
- PDB-5vyr: Crystal structure of the WbkC formyl transferase from Brucella me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vyr
TitleCrystal structure of the WbkC formyl transferase from Brucella melitensis
ComponentsGdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
KeywordsTRANSFERASE / N-formyltransferase / deoxysugar
Function / homology
Function and homology information


GDP-perosamine N-formyltransferase / methionyl-tRNA formyltransferase activity / lipopolysaccharide biosynthetic process / cytosol
Similarity search - Function
Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily
Similarity search - Domain/homology
Chem-B62 / GUANOSINE / GDP-perosamine N-formyltransferase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsRiegert, A.S. / Chantigian, D.P. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Biochemistry / Year: 2017
Title: Biochemical Characterization of WbkC, an N-Formyltransferase from Brucella melitensis.
Authors: Riegert, A.S. / Chantigian, D.P. / Thoden, J.B. / Tipton, P.A. / Holden, H.M.
History
DepositionMay 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
B: Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9339
Polymers58,6232
Non-polymers1,3107
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-29 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.875, 65.875, 233.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase


Mass: 29311.646 Da / Num. of mol.: 2 / Mutation: D78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI1418 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: F8WJP6, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases, GDP-mannose 4,6-dehydratase

-
Non-polymers , 5 types, 386 molecules

#2: Chemical ChemComp-B62 / (6R)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one


Mass: 181.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11N5O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18-22% PEG-5000, 5 mM GDP, 5 mM folinic acid, 100 mM MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 12, 2016 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 57143 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8645 / Rsym value: 0.308 / % possible all: 97

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.648 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 2807 4.9 %RANDOM
Rwork0.18478 ---
obs0.18721 54336 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.637 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 73 379 4326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194114
X-RAY DIFFRACTIONr_bond_other_d0.0010.023861
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9735597
X-RAY DIFFRACTIONr_angle_other_deg0.86538856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0045508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96423.01196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92215656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8781535
X-RAY DIFFRACTIONr_chiral_restr0.1080.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021015
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1681.9091978
X-RAY DIFFRACTIONr_mcbond_other2.1681.9081977
X-RAY DIFFRACTIONr_mcangle_it3.0782.8442471
X-RAY DIFFRACTIONr_mcangle_other3.0782.8452472
X-RAY DIFFRACTIONr_scbond_it3.0182.3272136
X-RAY DIFFRACTIONr_scbond_other3.0172.3272136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.683.3643116
X-RAY DIFFRACTIONr_long_range_B_refined6.42917.2145316
X-RAY DIFFRACTIONr_long_range_B_other6.42917.2215317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 186 -
Rwork0.286 3873 -
obs--96.9 %

+
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