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- PDB-2p9t: Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phospho... -

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Basic information

Entry
Database: PDB / ID: 2p9t
TitleCrystal Structure of Phosphoglycerate Kinase-2 bound to 3-phosphoglycerate
ComponentsPhosphoglycerate kinase, testis specific
KeywordsTRANSFERASE / phosphoglycerate kinse / enzyme-substrate complex
Function / homology
Function and homology information


sperm fibrous sheath / Glycolysis / Gluconeogenesis / phosphoglycerate kinase / phosphoglycerate kinase activity / flagellated sperm motility / gluconeogenesis / glycolytic process / ADP binding / cilium ...sperm fibrous sheath / Glycolysis / Gluconeogenesis / phosphoglycerate kinase / phosphoglycerate kinase activity / flagellated sperm motility / gluconeogenesis / glycolytic process / ADP binding / cilium / phosphorylation / extracellular exosome / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / Phosphoglycerate kinase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSawyer, G.M. / Monzingo, A.F. / Poteet, E.C. / Robertus, J.D.
CitationJournal: Proteins / Year: 2007
Title: X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus.
Authors: Sawyer, G.M. / Monzingo, A.F. / Poteet, E.C. / O'Brien, D.A. / Robertus, J.D.
History
DepositionMar 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence There is a Gln -> Arg sequence conflict at residue 151 in the Uniprot database. Authors ...sequence There is a Gln -> Arg sequence conflict at residue 151 in the Uniprot database. Authors state that Protein sequence used in this PDB entry is from C3H/He strain which has Arg at residue 150, whereas UniProt sequence is from BALB/c strain that has Gln at residue 151.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase, testis specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0242
Polymers44,8381
Non-polymers1861
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.100, 64.300, 72.200
Angle α, β, γ (deg.)90.000, 97.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoglycerate kinase, testis specific /


Mass: 44837.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C3H/He / Gene: Pgk2, Pgk-2 / Plasmid: PGK-2-pGEX4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09041, phosphoglycerate kinase
#2: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM D-3-phosphoglycerate, 30% PEG6000, 0.1 M Tris-Hcl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2006 / Details: BLUE MAX-FLUX CONFOCAL OPTICAL SYSTEM
RadiationMonochromator: BLUE MAX-FLUX CONFOCAL OPTICAL SYSTEM / Protocol: 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: 24578 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 6 % / Rmerge(I) obs: 0.209 / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VJD

1vjd


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1223 4.7 %RANDOM
Rwork0.221 ---
obs0.221 24465 94.4 %-
Solvent computationBsol: 43.21 Å2
Displacement parametersBiso mean: 24.62 Å2
Baniso -1Baniso -2Baniso -3
1--4.939 Å20 Å25.567 Å2
2--3.121 Å20 Å2
3---1.818 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 11 289 3418
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2081.5
X-RAY DIFFRACTIONc_mcangle_it1.7962
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.0082.5
LS refinement shellResolution: 2→2.03 Å / Total num. of bins used: 24
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION53PG.PAR3PG.TOP

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