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- PDB-1v7q: Crystal structure of phosphoglycerate mutase from Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 1v7q
TitleCrystal structure of phosphoglycerate mutase from Thermus thermophilus HB8
Componentsphosphoglycerate mutase
KeywordsISOMERASE / phosphoglycerate mutase / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


phosphatase activity / cytoplasm
Similarity search - Function
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
Alpha-ribazole-5'-phosphate phosphatase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of phosphoglycerate mutase from Thermus thermophilus HB8
Authors: Sugahara, M. / Kunishima, N.
History
DepositionDec 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phosphoglycerate mutase


Theoretical massNumber of molelcules
Total (without water)19,6281
Polymers19,6281
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.820, 42.820, 156.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

DetailsThe biological assembly is a monomer.

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Components

#1: Protein phosphoglycerate mutase


Mass: 19628.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q53WB3, EC: 5.4.2.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.27 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.3
Details: sodium acetate, pH 6.3, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 29, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→40 Å / Num. all: 20623 / Num. obs: 20623 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.044 / Net I/σ(I): 12.3
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 5 / Num. unique all: 2000 / Rsym value: 0.438 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V37

1v37


Resolution: 1.59→37.57 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1032 -RANDOM
Rwork0.222 ---
all0.223 20513 --
obs0.223 20513 99.8 %-
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å20 Å2
2--2.39 Å20 Å2
3----4.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.59→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 0 127 1462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.59→1.65 Å / Rfactor Rfree error: 0.033
RfactorNum. reflection% reflection
Rfree0.33 102 -
Rwork0.281 --
obs-1908 100 %

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