[English] 日本語
Yorodumi
- PDB-3gp3: Crystal structure of phosphoglyceromutase from Burkholderia pseud... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gp3
TitleCrystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 2-phosphoserine
Components2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
KeywordsISOMERASE / phosphoglyceromutase / deCODE / SBRI / NIAID / UWPPG / Glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / PHOSPHOSERINE / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase.
Authors: Davies, D.R. / Staker, B.L. / Abendroth, J.A. / Edwards, T.E. / Hartley, R. / Leonard, J. / Kim, H. / Rychel, A.L. / Hewitt, S.N. / Myler, P.J. / Stewart, L.J.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
C: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
D: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,05718
Polymers115,8354
Non-polymers2,22214
Water12,827712
1
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4174
Polymers28,9591
Non-polymers4583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4174
Polymers28,9591
Non-polymers4583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6115
Polymers28,9591
Non-polymers6524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6115
Polymers28,9591
Non-polymers6524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.263, 72.045, 78.036
Angle α, β, γ (deg.)107.960, 93.000, 104.200
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / Phosphoglyceromutase / PGAM / BPG-dependent PGAM / dPGM


Mass: 28958.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expressed with a non-cleavable N-terminal hexahis-tag
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: gpmA, BPSL0443 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63XU7, UniProt: Q3JWH7*PLUS, EC: 5.4.2.1
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO3
#4: Chemical
ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EMERALD CRYO B-4: 100MM MES PH 7.5, 5% PEG 1000, 10% GLYCEROL, 30% PEG 600, 11.7 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorDate: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 149575 / % possible obs: 95.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.081 / Χ2: 1.703 / Net I/σ(I): 18.062
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.4 / Num. unique all: 13280 / Χ2: 1.481 / % possible all: 84.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.72 Å39.88 Å
Translation1.72 Å39.88 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.574 / SU B: 1.939 / SU ML: 0.07 / SU R Cruickshank DPI: 0.101 / SU Rfree: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.268 7460 5 %RANDOM
Rwork0.237 ---
obs0.238 148953 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.79 Å2 / Biso mean: 19.203 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0.12 Å20.21 Å2
2--0.03 Å20.53 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7298 0 138 712 8148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0227747
X-RAY DIFFRACTIONr_bond_other_d0.0010.025279
X-RAY DIFFRACTIONr_angle_refined_deg2.1141.97410554
X-RAY DIFFRACTIONr_angle_other_deg1.099312812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5715944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28423.184358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05615.0481246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9721568
X-RAY DIFFRACTIONr_chiral_restr0.1390.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021574
X-RAY DIFFRACTIONr_mcbond_it1.4011.54692
X-RAY DIFFRACTIONr_mcbond_other0.4681.51870
X-RAY DIFFRACTIONr_mcangle_it2.26627576
X-RAY DIFFRACTIONr_scbond_it3.46533055
X-RAY DIFFRACTIONr_scangle_it5.3344.52978
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 474 -
Rwork0.429 8972 -
all-9446 -
obs--81.72 %

+
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