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- PDB-1e59: E.coli cofactor-dependent phosphoglycerate mutase complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1.0E+59
TitleE.coli cofactor-dependent phosphoglycerate mutase complexed with vanadate
ComponentsPHOSPHOGLYCERATE MUTASE
KeywordsISOMERASE / INHIBITOR / VANDATE / GLYCOLYSIS AND GLUCONEOGENESIS / PHOSPHOGLYCERATE MUTASE
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / canonical glycolysis / guanosine tetraphosphate binding / gluconeogenesis / protein homodimerization activity / ATP binding / cytosol / cytoplasm
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
TETRAMETAVANADATE / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBond, C.S. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Mechanistic Implications for Escherichia Coli Cofactor-Dependent Phosphoglycerate Mutase Based on the High-Resolution Crystal Structure of a Vanadate Complex.
Authors: Bond, C.S. / White, M. / Hunter, W.N.
History
DepositionJul 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOGLYCERATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9123
Polymers28,4651
Non-polymers4472
Water4,756264
1
A: PHOSPHOGLYCERATE MUTASE
hetero molecules

A: PHOSPHOGLYCERATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8256
Polymers56,9302
Non-polymers8944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.249, 112.142, 40.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PHOSPHOGLYCERATE MUTASE


Mass: 28465.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Gene: PGM1 / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P31217, UniProt: P62707*PLUS, EC: 5.4.2.1
#2: Chemical ChemComp-VO3 / TETRAMETAVANADATE


Mass: 411.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O13V4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: 2-PHOSPHOGLYCERATE + 2,3-DIPHOSPHOGLYCERATE = 3-PHOSPHOGLYCERATE + 2,3- ...CATALYTIC ACTIVITY: 2-PHOSPHOGLYCERATE + 2,3-DIPHOSPHOGLYCERATE = 3-PHOSPHOGLYCERATE + 2,3-DIPHOSPHOGLYCERATE. PATHWAY: GLYCOLYSIS. SIMILARITY: BELONGS TO THE PHOSPHOGLYCERATE MUTASE FAMILY.

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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: 2.21 Å3/Da / Density % sol: 51 %
Crystal growpH: 8.5
Details: 100 MM TRIS-HCL (PH 8.0), 200 MM LI2SO4, 20% PEG 4000, 100 MM NAVO3
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
3100 mM1dropNaCl
4100 mMTris-HCl1reservoirpH8.75
5200 mM1reservoirLi2SO4
620 %(w/v)PEG40001reservoir
7100 mM1reservoirNaVO3

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.89
DetectorDate: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 68073 / % possible obs: 96.6 % / Redundancy: 4 % / Rsym value: 0.079 / Net I/σ(I): 17
Reflection shellResolution: 1.3→1.31 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.401 / % possible all: 99.9
Reflection
*PLUS
Redundancy: 3.1 % / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.401

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E58

1e58


Resolution: 1.3→30 Å / Num. parameters: 20185 / Num. restraintsaints: 24690 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: VO3 VALUES EXTRACTED FROM CSDS
Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 2061 3.1 %RANDOM
all0.1591 65738 --
obs0.1552 -96.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2210.5
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 18 264 2227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0294
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.087
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1552
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.0294
X-RAY DIFFRACTIONs_chiral_restr0.059

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