[English] 日本語
Yorodumi
- PDB-7m15: crystal structure of cj1430 in the presence of GDP-D-glycero-L-gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m15
Titlecrystal structure of cj1430 in the presence of GDP-D-glycero-L-gluco-heptose, a GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase from campylobacter jejuni
ComponentsGDP-D-glycero-L-gluco-heptose
KeywordsISOMERASE / 3 / 5-epimerase / capsular polysaccharide
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / polysaccharide biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Chem-YO7 / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGirardi, N.M. / Thoden, J.B. / Raushel, F.M. / Holden, H.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122825 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134643 United States
Robert A. Welch FoundationA-840 United States
CitationJournal: Biochemistry / Year: 2021
Title: Biosynthesis of d- glycero -l- gluco -Heptose in the Capsular Polysaccharides of Campylobacter jejuni .
Authors: Huddleston, J.P. / Anderson, T.K. / Girardi, N.M. / Thoden, J.B. / Taylor, Z. / Holden, H.M. / Raushel, F.M.
History
DepositionMar 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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: GDP-D-glycero-L-gluco-heptose
B: GDP-D-glycero-L-gluco-heptose
C: GDP-D-glycero-L-gluco-heptose
D: GDP-D-glycero-L-gluco-heptose
E: GDP-D-glycero-L-gluco-heptose
F: GDP-D-glycero-L-gluco-heptose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,31417
Polymers128,1926
Non-polymers4,12311
Water14,646813
1
A: GDP-D-glycero-L-gluco-heptose
B: GDP-D-glycero-L-gluco-heptose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0635
Polymers42,7312
Non-polymers1,3333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-15 kcal/mol
Surface area15750 Å2
MethodPISA
2
C: GDP-D-glycero-L-gluco-heptose
D: GDP-D-glycero-L-gluco-heptose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0635
Polymers42,7312
Non-polymers1,3333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-11 kcal/mol
Surface area15890 Å2
MethodPISA
3
E: GDP-D-glycero-L-gluco-heptose
F: GDP-D-glycero-L-gluco-heptose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1887
Polymers42,7312
Non-polymers1,4575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-12 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.409, 81.569, 109.453
Angle α, β, γ (deg.)90.000, 94.380, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
GDP-D-glycero-L-gluco-heptose


Mass: 21365.320 Da / Num. of mol.: 6 / Mutation: K128A, E129A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: rfbC, Cj1430c / Production host: Escherichia coli (E. coli)
References: UniProt: Q0P8I4, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-YO7 / [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name)


Mass: 635.367 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H27N5O17P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22-27% PEG-5000, 100 mM MOPS, 10 mM GDP-D-glycero-L-gluco-heptose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 99769 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.083 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 13932 / Rsym value: 0.389 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7m14

7m14


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.301 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 5212 5.2 %RANDOM
Rwork0.1901 ---
obs0.1924 94557 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.34 Å2 / Biso mean: 16.551 Å2 / Biso min: 2.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20.06 Å2
2--1.11 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8859 0 266 813 9938
Biso mean--13.04 22.1 -
Num. residues----1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139396
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178437
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.68812798
X-RAY DIFFRACTIONr_angle_other_deg1.2781.59919632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.71251071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22523.074475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.361151556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9051536
X-RAY DIFFRACTIONr_chiral_restr0.0720.21237
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021980
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 375 -
Rwork0.352 6621 -
all-6996 -
obs--93.4 %

+
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