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- PDB-2h4z: Human bisphosphoglycerate mutase complexed with 2,3-bisphosphogly... -

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Basic information

Entry
Database: PDB / ID: 2h4z
TitleHuman bisphosphoglycerate mutase complexed with 2,3-bisphosphoglycerate
ComponentsBisphosphoglycerate mutase
KeywordsISOMERASE / BISPHOSPHOGLYCERATE MUTASE / 2 / 3-BISPHOSPHOGLYCERATE
Function / homology
Function and homology information


carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / neuroinflammatory response / respiratory gaseous exchange by respiratory system / establishment of blood-brain barrier / Glycolysis / cellular response to stress ...carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / neuroinflammatory response / respiratory gaseous exchange by respiratory system / establishment of blood-brain barrier / Glycolysis / cellular response to stress / defense response to protozoan / erythrocyte development / oxygen transport / glycolytic process / carbohydrate metabolic process / hydrolase activity / extracellular exosome / cytosol
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
(2R)-2,3-diphosphoglyceric acid / Bisphosphoglycerate mutase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Y. / Gong, W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase.
Authors: Wang, Y. / Liu, L. / Wei, Z. / Cheng, Z. / Lin, Y. / Gong, W.
History
DepositionMay 25, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2016Group: Non-polymer description
Revision 1.4Oct 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: Bisphosphoglycerate mutase
B: Bisphosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7694
Polymers62,2372
Non-polymers5322
Water9,998555
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.096, 71.229, 159.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bisphosphoglycerate mutase / 2 / 3-bisphosphoglycerate mutase / erythrocyte / 2 / 3-bisphosphoglycerate synthase / BPGM / BPG- ...2 / 3-bisphosphoglycerate mutase / erythrocyte / 2 / 3-bisphosphoglycerate synthase / BPGM / BPG-dependent PGAM


Mass: 31118.375 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: P07738, bisphosphoglycerate mutase, EC: 5.4.2.1, EC: 3.1.3.13
#2: Chemical ChemComp-DG2 / (2R)-2,3-diphosphoglyceric acid / 2,3-Bisphosphoglyceric acid / 2,3-bisphosphoglycerate / 2,3-BPG / 2,3-diphosphoglyceric acid / 2,3-diphosphoglycerate / 2,3-DPG / (2~{R})-2,3-diphosphonooxypropanoic acid


Mass: 266.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.12 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 277 K / pH: 7
Details: PEG6000, HEPES , VAPOR DIFFUSION, HANGING DROP, pH 7.00, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 37662 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.6 / % possible all: 95.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T8P

1t8p


Resolution: 2→28.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 255021.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1805 5 %RANDOM
Rwork0.184 ---
obs0.184 36127 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.81 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-13.3 Å20 Å20 Å2
2---5.18 Å20 Å2
3----8.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 30 555 4685
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 294 5.2 %
Rwork0.239 5336 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DPG.PARAMDPG.TOP

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