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- PDB-1v37: Crystal structure of phosphoglycerate mutase from Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 1v37
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


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 / SIR / Resolution: 1.4 Å
AuthorsSugahara, M. / Yokoyama, S. / Kuramitsu, S. / Miyano, M. / Iizuka, T. / 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. / Yokoyama, S. / Kuramitsu, S. / Miyano, M. / Iizuka, T. / Kunishima, N.
History
DepositionOct 29, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phosphoglycerate mutase
B: phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4414
Polymers39,2572
Non-polymers1842
Water6,792377
1
A: phosphoglycerate mutase
B: phosphoglycerate mutase
hetero molecules

A: phosphoglycerate mutase
B: phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8828
Polymers78,5144
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)84.591, 91.846, 110.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit.

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Components

#1: Protein phosphoglycerate mutase /


Mass: 19628.465 Da / Num. of mol.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.49 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.3
Details: sodium chloride, pH 8.3, 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: Sep 25, 2003 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 84540 / Num. obs: 84540 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.13 % / Biso Wilson estimate: 14.204 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.073 / Net I/σ(I): 9.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.1 / Num. unique all: 8370 / Rsym value: 0.525 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SIR / Resolution: 1.4→37.92 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4242 -RANDOM
Rwork0.206 ---
all0.207 84540 --
obs0.207 84540 99.6 %-
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---1.61 Å20 Å2
3---0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.4→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 12 377 3083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.4→1.45 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.281 429 -
Rwork0.264 --
obs-7737 97.2 %

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