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

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Basic information

Entry
Database: PDB / ID: 2hhj
TitleHuman bisphosphoglycerate mutase complexed with 2,3-bisphosphoglycerate (15 days)
ComponentsBisphosphoglycerate mutase
KeywordsISOMERASE / BISPHOSPHOGLYCERATE MUTASE / 2 / 3-BISPHOSPHOGLYCERATE
Function / homology
Function and homology information


carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / erythrocyte development ...carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / erythrocyte development / defense response to protozoan / oxygen transport / glycolytic process / hydrolase activity / carbohydrate metabolic process / 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
3-PHOSPHOGLYCERIC ACID / (2R)-2,3-diphosphoglyceric acid / CYCLOHEXYLAMMONIUM ION / Bisphosphoglycerate mutase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionJun 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bisphosphoglycerate mutase
B: Bisphosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3997
Polymers62,3952
Non-polymers1,0045
Water13,691760
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.692, 71.555, 159.194
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: 31197.344 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-HAI / CYCLOHEXYLAMMONIUM ION / Cyclohexylamine


Mass: 100.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N
#3: 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 / 2,3-Bisphosphoglyceric acid


Mass: 266.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O10P2
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(DG2, NEP) (DG2, 3PG) ARE PARTIALLY IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG6000, TEMPERATURE 289K, pH 7.50, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 88158 / Num. obs: 88158 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.76 / % possible all: 92.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.83 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 387209.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 8399 10 %RANDOM
Rwork0.182 ---
all0.185 ---
obs0.182 83760 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.32 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1-5.22 Å20 Å20 Å2
2---3.12 Å20 Å2
3----2.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4143 0 59 760 4962
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 1231 10 %
Rwork0.241 11098 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HAI.PARAMHAI.TOP
X-RAY DIFFRACTION43PGA.PARAM3PGA.TOP
X-RAY DIFFRACTION5DPG.PARAMPI.TOP

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