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- PDB-3c3a: Crystal Structure of human phosphoglycerate kinase bound to 3-pho... -

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Basic information

Entry
Database: PDB / ID: 3c3a
TitleCrystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-ADP
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE / protein-nucleotide complex / L-enantiomer of ADP / kinase / Acetylation / ATP-binding / Cytoplasm / Disease mutation / Glycolysis / Hereditary hemolytic anemia / Nucleotide-binding / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / phosphorylation / epithelial cell differentiation ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / phosphorylation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / membrane raft / 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
3-PHOSPHOGLYCERIC ACID / ADENOSINE-5'-DIPHOSPHATE / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Nov 6, 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)90,7336
Polymers89,9102
Non-polymers8244
Water5,765320
1
A: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1412
Polymers44,9551
Non-polymers1861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5924
Polymers44,9551
Non-polymers6383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.629, 55.949, 95.441
Angle α, β, γ (deg.)101.88, 95.20, 82.91
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-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.01 %
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: 0.934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2006
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→51.64 Å / Num. all: 26390 / Num. obs: 26390 / % possible obs: 84.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2383 / % possible all: 55.3

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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: 2.3→43.2 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.861 / SU B: 9.032 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.283 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27789 551 2 %RANDOM
Rwork0.17876 ---
obs0.18084 26389 84.87 %-
all-26389 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.422 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20.03 Å20 Å2
2--0.01 Å2-0.02 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 50 320 6411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226183
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.631.998333
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.49625.647232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.425151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8781522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214487
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_it0.98123971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82436351
X-RAY DIFFRACTIONr_scbond_it4.15262212
X-RAY DIFFRACTIONr_scangle_it6.408101982
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 18 -
Rwork0.178 1195 -
obs--51.33 %

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