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- PDB-1yfk: Crystal structure of human B type phosphoglycerate mutase -

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Basic information

Entry
Database: PDB / ID: 1yfk
TitleCrystal structure of human B type phosphoglycerate mutase
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE / HYDROLASE / alpha/beta
Function / homology
Function and homology information


phosphoglycerate mutase activity / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...phosphoglycerate mutase activity / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / membrane / 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
CITRIC ACID / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, Y. / Wei, Z. / Liu, L. / Gong, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Crystal structure of human B-type phosphoglycerate mutase bound with citrate.
Authors: Wang, Y. / Wei, Z. / Liu, L. / Cheng, Z. / Lin, Y. / Ji, F. / Gong, W.
History
DepositionJan 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: Phosphoglycerate mutase 1
B: Phosphoglycerate mutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2545
Polymers59,8342
Non-polymers4203
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-10 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.861, 65.745, 124.812
Angle α, β, γ (deg.)90.00, 94.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoglycerate mutase 1 / Phosphoglycerate mutase isozyme B / PGAM-B / BPG-dependent PGAM 1


Mass: 29917.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P18669, EC: 5.4.2.1, bisphosphoglycerate mutase, EC: 3.1.3.13
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.57 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, (NH4)2SO4, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 17981 / Num. obs: 17981 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.129
Reflection shellResolution: 2.7→2.76 Å / Rmerge(I) obs: 0.436 / % possible all: 94.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5PGM

5pgm


Resolution: 2.7→29.07 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 216724.15 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 671 3.9 %RANDOM
Rwork0.216 ---
all0.218 17105 --
obs0.216 17105 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.8217 Å2 / ksol: 0.318037 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-17.01 Å20 Å212.34 Å2
2---1.68 Å20 Å2
3----15.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 27 121 3949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 97 3.9 %
Rwork0.323 2389 -
obs--78.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIT_XPLOR_PAR.TXTCIT_XPLOR_TOP.TXT
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER.TOP

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