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- PDB-1rii: Crystal structure of phosphoglycerate mutase from M. Tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1rii
TitleCrystal structure of phosphoglycerate mutase from M. Tuberculosis
Components2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
KeywordsISOMERASE / Phosphoglyerate Mutase / SH3 Domain Binding / Structural genomics / TBSGC / Protein Structure Initiative / PSI / TB Structural Genomics Consortium
Function / homology
Function and homology information


: / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / glycolytic process / gluconeogenesis / protein-containing complex / identical protein binding / plasma membrane
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
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMueller, P. / Sawaya, M.R. / Chan, S. / Wu, Y. / Pashkova, I. / Perry, J. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase.
Authors: Muller, P. / Sawaya, M.R. / Pashkov, I. / Chan, S. / Nguyen, C. / Wu, Y. / Perry, L.J. / Eisenberg, D.
History
DepositionNov 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 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)116,4599
Polymers115,9994
Non-polymers4605
Water8,125451
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.914, 136.790, 65.929
Angle α, β, γ (deg.)90.00, 97.78, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the homotetramer formed by the chains A, B, C and D which forms the asymmetric unit.

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Components

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


Mass: 28999.678 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: GPMA, GPM, PGM, GPM1, RV0489, MT0508, MTCY20G9.15, MB0499
Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
References: UniProt: P0A5R6, UniProt: P9WIC9*PLUS, EC: 5.4.2.1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.51 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 298 K / pH: 7
Details: 15% PEG 3350, 0.1M magnesium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2003
RadiationMonochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→58.37 Å / Num. obs: 111293 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 21.33 Å2 / Rsym value: 0.0699 / Net I/σ(I): 18.1
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.4548 / % possible all: 91.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SADABS(SHELDRICKdata reduction
GLRFphasing
SHELXL-97refinement
SADABSV. 2003 (SHELDRICK)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5PGM

5pgm


Resolution: 1.7→58.37 Å / Num. parameters: 31673 / Num. restraintsaints: 31045 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. HYDROGENS HAVE BEEN ADDED AT GEOMETRICALLY CALCULATED POSITIONS AND REFINED USING A RIDING MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 2664 2.5 %RANDOM
all0.2206 111293 --
obs0.2193 -98.2 %-
Solvent computationSolvent model: Bulk solvent was treated following the Babinet-Principle refining two parameters, using the SWAT command in SHELXL.
Displacement parametersBiso mean: 33.8 Å2
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 6617 / Occupancy sum non hydrogen: 7846
Refinement stepCycle: LAST / Resolution: 1.7→58.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 30 451 7849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.028
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.7→1.8 Å /
Num. reflection% reflection
Rfree409 -
obs-91.8 %

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