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- PDB-3c3b: Crystal Structure of human phosphoglycerate kinase bound to D-CDP -

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Basic information

Entry
Database: PDB / ID: 3c3b
TitleCrystal Structure of human phosphoglycerate kinase bound to D-CDP
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE / protein-nucleotide complex / D-enantiomer of CDP / kinase / Acetylation / ATP-binding / Cytoplasm / Disease mutation / Glycolysis / Hereditary hemolytic anemia / Nucleotide-binding / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


negative regulation of pyruvate decarboxylation to acetyl-CoA / Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase [NAD(P)H] activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation ...negative regulation of pyruvate decarboxylation to acetyl-CoA / Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase [NAD(P)H] activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / non-specific serine/threonine protein kinase / mitochondrial matrix / membrane raft / protein serine/threonine kinase activity / extracellular space / extracellular exosome / ATP binding / membrane / 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
CYTIDINE-5'-DIPHOSPHATE / PHOSPHATE ION / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArold, S.T. / Gondeau, C. / Lionne, C. / Chaloin, L.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase
Authors: Gondeau, C. / Chaloin, L. / Lallemand, P. / Roy, B. / Perigaud, C. / Barman, T. / Varga, A. / Vas, M. / Lionne, C. / Arold, S.T.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase 1
B: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5035
Polymers89,9102
Non-polymers5933
Water13,295738
1
A: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0502
Polymers44,9551
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4533
Polymers44,9551
Non-polymers4982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.579, 55.588, 93.805
Angle α, β, γ (deg.)78.92, 84.32, 82.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Phosphoglycerate kinase 1 / 3-Phosphoglycerate Kinase / Primer recognition protein 2 / PRP 2 / Cell migration-inducing gene 10 protein


Mass: 44954.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGK1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)/pDIA17 / References: UniProt: P00558, phosphoglycerate kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 38.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 2.6M NaKPO4, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2007
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→50.96 Å / Num. all: 54699 / Num. obs: 54699 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / Num. unique all: 3838 / % possible all: 50.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJC

1vjc


Resolution: 1.8→50.94 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.324 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1703 3 %RANDOM
Rwork0.16925 ---
all0.17137 54697 --
obs0.17137 54697 87.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.435 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.01 Å20 Å2
2---0.03 Å20.01 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 35 738 6777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226129
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg21.9898258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8865796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.31625.633229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.865151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4811522
X-RAY DIFFRACTIONr_chiral_restr0.1520.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214447
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.75323955
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.80336323
X-RAY DIFFRACTIONr_scbond_it5.59562174
X-RAY DIFFRACTIONr_scangle_it8.451101935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 58 -
Rwork0.244 2084 -
obs--44.82 %

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