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- PDB-1e58: E.coli cofactor-dependent phosphoglycerate mutase -

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Basic information

Entry
Database: PDB / ID: 1.0E+58
TitleE.coli cofactor-dependent phosphoglycerate mutase
ComponentsPHOSPHOGLYCERATE MUTASE
KeywordsISOMERASE / PHOSPHOHISTIDINE / GLYCOLYSIS AND GLUCONEOGENESIS / PHOSPHOGLYCERATE MUTASE
Function / homology
Function and homology information


2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 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
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBond, C.S. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: High Resolution Structure of the Phosphohistidine-Activated Form of Escherichia Coli Cofactor-Dependent Phosphoglycerate Mutase.
Authors: Bond, C.S. / White, M.F. / Hunter, W.N.
History
DepositionJul 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2001Provider: 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: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag

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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)28,7724
Polymers28,5441
Non-polymers2283
Water7,656425
1
A: PHOSPHOGLYCERATE MUTASE
hetero molecules

A: PHOSPHOGLYCERATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5438
Polymers57,0882
Non-polymers4556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1700 Å2
ΔGint-2.7 kcal/mol
Surface area27000 Å2
MethodPQS
Unit cell
Length a, b, c (Å)61.570, 113.000, 40.260
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: 28544.164 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: P62707, EC: 5.4.2.1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.14 Å3/Da / Density % sol: 51 %
Crystal growpH: 8.5
Details: 100 MM TRIS-HCL (PH 8.0), 200 MM LI2SO4, 20% PEG 4000
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mM1dropNaCl
4100 mMTris-HCl1reservoir
5200 mM1reservoirLiSO4
620 %PEG40001reservoir

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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: 1.25→30 Å / Num. obs: 67122 / % possible obs: 85.4 % / Redundancy: 2 % / Rsym value: 0.047 / Net I/σ(I): 211
Reflection shellResolution: 1.25→1.26 Å / Redundancy: 2 % / Mean I/σ(I) obs: 11 / Rsym value: 0.071 / % possible all: 63
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 63 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 11.2

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.25→10 Å / Num. parameters: 22606 / Num. restraintsaints: 27457 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56 PHOSPHOHISTIDINE MODELLED AT 0.28 OCCUPANCY COUPLED TO A 0.72 OCCUPANCY HISTIDINE WITH THREE WATER MOLECULES
RfactorNum. reflection% reflectionSelection details
Rfree0.168 -3 %RANDOM
all0.1209 65026 --
obs0.121 -83 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 1977 / Occupancy sum non hydrogen: 2434.16
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 11 425 2437
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0314
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.076
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.08
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14 Å2

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