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- PDB-2paa: Crystal structure of phosphoglycerate kinase-2 bound to atp and 3pg -

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Basic information

Entry
Database: PDB / ID: 2paa
TitleCrystal structure of phosphoglycerate kinase-2 bound to atp and 3pg
ComponentsPhosphoglycerate kinase, testis specific
KeywordsTRANSFERASE / phosphoglycerate kinase / enzyme-ligand complex
Function / homology
Function and homology information


Gluconeogenesis / sperm fibrous sheath / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / flagellated sperm motility / phosphorylation / gluconeogenesis / glycolytic process / ADP binding ...Gluconeogenesis / sperm fibrous sheath / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / flagellated sperm motility / phosphorylation / gluconeogenesis / glycolytic process / ADP binding / cilium / 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 / ADENOSINE-5'-TRIPHOSPHATE / Phosphoglycerate kinase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 27, 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
B: Phosphoglycerate kinase, testis specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3694
Polymers89,6762
Non-polymers6932
Water50428
1
A: Phosphoglycerate kinase, testis specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3452
Polymers44,8381
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoglycerate kinase, testis specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0242
Polymers44,8381
Non-polymers1861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.854, 64.541, 75.936
Angle α, β, γ (deg.)90.340, 77.200, 85.030
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Phosphoglycerate kinase, testis specific


Mass: 44837.836 Da / Num. of mol.: 2
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% PEG6000, 0.1 M bicine, 10 mM 3-D-phosphoglycerate, 5 mM ATP, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 6, 2006 / Details: BLUE MAX-FLUX CONFOCAL
RadiationMonochromator: BLUE MAX-FLUX CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 19197 / % possible obs: 96.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.056 / Χ2: 1.114 / Net I/σ(I): 14.7
Reflection shellResolution: 2.7→2.81 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.125 / Num. unique all: 1839 / Χ2: 0.815 / % possible all: 91.7

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Processing

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

1vjd


Resolution: 2.7→20 Å / FOM work R set: 0.807 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 947 4.7 %random
Rwork0.197 ---
obs-18535 92.1 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 21.659 Å2
Baniso -1Baniso -2Baniso -3
1--5.533 Å2-2.568 Å24.712 Å2
2--2.378 Å21.551 Å2
3---3.154 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 42 28 6125
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.405
X-RAY DIFFRACTIONc_mcbond_it1.2481.5
X-RAY DIFFRACTIONc_scbond_it1.7762
X-RAY DIFFRACTIONc_mcangle_it2.1172
X-RAY DIFFRACTIONc_scangle_it2.7192.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.750.369240.31538562
2.75-2.810.415560.2949731029
2.81-2.870.298600.248903963
2.87-2.940.342470.2519711018
2.94-3.010.312430.2439701013
3.01-3.090.308560.2399731029
3.09-3.180.32460.2259831029
3.18-3.280.3620.21910161078
3.28-3.40.308630.2439631026
3.4-3.530.307530.21310141067
3.53-3.690.253490.16510301079
3.69-3.890.305520.19610251077
3.89-4.130.25570.16210261083
4.13-4.440.261570.17910571114
4.44-4.890.203600.13610201080
4.89-5.580.237520.19710301082
5.58-6.980.217540.18310351089
6.98-200.175560.13310611117
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 DIFFRACTION5atp-3pg.paratp-3pg.top

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