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- PDB-6hxe: Crystal structure of psychrophilic phosphoglycerate kinase from P... -

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Basic information

Entry
Database: PDB / ID: 6hxe
TitleCrystal structure of psychrophilic phosphoglycerate kinase from Pseudomonas TACII18 in complex with 3-phosphoglycerate
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / Complex / 3-phosphoglycerate / hinge binding
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm
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
Similarity search - Component
Biological speciesPseudomonas sp. 'TAC II 18' (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMandelman, D. / Haser, R. / Aghajari, N.
Funding support France, 1items
OrganizationGrant numberCountry
European UnionCT970131 France
Citation
Journal: Extremophiles / Year: 2019
Title: Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase.
Authors: Mandelman, D. / Ballut, L. / Wolff, D.A. / Feller, G. / Gerday, C. / Haser, R. / Aghajari, N.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2001
Title: Crystallization and preliminary X-ray analysis of a bacterial psychrophilic enzyme, phosphoglycerate kinase.
Authors: Mandelman, D. / Bentahir, M. / Feller, G. / Gerday, C. / Haser, R.
History
DepositionOct 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4532
Polymers40,2671
Non-polymers1861
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-3 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 58.500, 85.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Phosphoglycerate kinase /


Mass: 40267.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: There is a mismatch between the sequence deposited in uniprot (ID: Q9RBS3) and the structure at position 150. This should clearly be a Ser as judged from the electron density and not a Pro ...Details: There is a mismatch between the sequence deposited in uniprot (ID: Q9RBS3) and the structure at position 150. This should clearly be a Ser as judged from the electron density and not a Pro as listed in the sequence. Idem for residue 219 which is not a Ser but an Asp and residue 358 which is not a Tyr but a Gln. Following residues have been refined as alanines due to missing electron density for the side-chains: 27, 102, 243, 248, 268, 292, 327, 348
Source: (gene. exp.) Pseudomonas sp. 'TAC II 18' (bacteria) / Gene: pgk / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RBS3, 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.: 267 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 30% polyethylene glycol (PEG) 4000, 0.2 M MgCl2 and 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1999
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→46 Å / Num. obs: 61709 / % possible obs: 99.4 % / Redundancy: 3.3 % / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vpe

1vpe


Resolution: 2.1→16.887 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.52
RfactorNum. reflection% reflection
Rfree0.2219 1233 5.1 %
Rwork0.1742 --
obs0.1766 24170 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→16.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 11 267 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072827
X-RAY DIFFRACTIONf_angle_d0.8183846
X-RAY DIFFRACTIONf_dihedral_angle_d3.0711694
X-RAY DIFFRACTIONf_chiral_restr0.052470
X-RAY DIFFRACTIONf_plane_restr0.005500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8995-1.97550.3895820.32641529X-RAY DIFFRACTION57
1.9755-2.06520.28551320.26752510X-RAY DIFFRACTION92
2.0652-2.17390.28631450.23582699X-RAY DIFFRACTION99
2.1739-2.30980.27991340.20232701X-RAY DIFFRACTION99
2.3098-2.48760.25681550.19252677X-RAY DIFFRACTION100
2.4876-2.7370.25931380.1912733X-RAY DIFFRACTION100
2.737-3.13090.22231570.17882696X-RAY DIFFRACTION100
3.1309-3.93630.18761500.14422721X-RAY DIFFRACTION100
3.9363-16.88820.18181400.14392671X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 55.225 Å / Origin y: 6.5017 Å / Origin z: 0.8257 Å
111213212223313233
T0.1988 Å2-0.0064 Å2-0.012 Å2-0.2597 Å2-0.0014 Å2--0.2 Å2
L0.9987 °20.3079 °2-0.161 °2-0.776 °2-0.4221 °2--0.6037 °2
S-0.0726 Å °0.1273 Å °0.0669 Å °0.0136 Å °0.1269 Å °0.0641 Å °0.0151 Å °-0.0914 Å °-0.0613 Å °
Refinement TLS groupSelection details: all

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