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- PDB-6i06: Crystal structure of psychrophilic phosphoglycerate kinase from P... -

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Basic information

Entry
Database: PDB / ID: 6i06
TitleCrystal structure of psychrophilic phosphoglycerate kinase from Pseudomonas TACII18
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / hinge binding / kinase / glycolysis
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
Phosphoglycerate kinase
Similarity search - Component
Biological speciesPseudomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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 25, 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


Theoretical massNumber of molelcules
Total (without water)40,3021
Polymers40,3021
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 59.100, 87.000
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: 40302.250 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: Q12, K102, K116 and the K248 has been refined as a Ser and Ser266 as a Gly due to missing electron density
Source: (gene. exp.) Pseudomonas (bacteria) / Gene: pgk / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RBS3, phosphoglycerate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 10000 and 0.1 M HEPES at pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.90005 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90005 Å / Relative weight: 1
ReflectionResolution: 2→29.55 Å / Num. obs: 23306 / % possible obs: 99.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12
Reflection shellResolution: 2→2.09 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6HXE

6hxe


Resolution: 2→29.55 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 23.2
RfactorNum. reflection% reflection
Rfree0.2289 1170 5.1 %
Rwork0.179 --
obs0.1815 22952 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 0 220 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022850
X-RAY DIFFRACTIONf_angle_d0.4793874
X-RAY DIFFRACTIONf_dihedral_angle_d2.2192327
X-RAY DIFFRACTIONf_chiral_restr0.042470
X-RAY DIFFRACTIONf_plane_restr0.003503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.09120.28081500.22082732X-RAY DIFFRACTION100
2.0912-2.20140.28231400.21912736X-RAY DIFFRACTION100
2.2014-2.33920.27211410.19792715X-RAY DIFFRACTION100
2.3392-2.51980.25591510.21642702X-RAY DIFFRACTION100
2.5198-2.77320.26461420.20992741X-RAY DIFFRACTION100
2.7732-3.1740.26541530.19872699X-RAY DIFFRACTION100
3.174-3.99740.2031510.1612733X-RAY DIFFRACTION100
3.9974-29.55320.18421420.1462724X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 55.0185 Å / Origin y: 6.3529 Å / Origin z: 0.4371 Å
111213212223313233
T0.1232 Å2-0.0269 Å2-0.0057 Å2-0.1871 Å20.0021 Å2--0.1107 Å2
L0.4583 °2-0.108 °2-0.3818 °2-0.5808 °2-0.0898 °2--0.1516 °2
S0.1257 Å °-0.0381 Å °0.0517 Å °-0.0404 Å °-0.1199 Å °-0.0266 Å °-0.0146 Å °-0.0509 Å °0.0005 Å °
Refinement TLS groupSelection details: all

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