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- PDB-1yvy: Crystal structure of Anaerobiospirillum succiniciproducens phosph... -

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Basic information

Entry
Database: PDB / ID: 1yvy
TitleCrystal structure of Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase
ComponentsPhosphoenolpyruvate carboxykinase [ATP]
KeywordsLYASE / p-loop / domain movement / kinase / succinate
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal ...Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesAnaerobiospirillum succiniciproducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCotelesage, J.J. / Prasad, L. / Zeikus, J.G. / Laivenieks, M. / Delbaere, L.T.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2005
Title: Crystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop.
Authors: Cotelesage, J.J. / Prasad, L. / Zeikus, J.G. / Laivenieks, M. / Delbaere, L.T.
History
DepositionFeb 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Phosphoenolpyruvate carboxykinase [ATP]
B: Phosphoenolpyruvate carboxykinase [ATP]


Theoretical massNumber of molelcules
Total (without water)117,4192
Polymers117,4192
Non-polymers00
Water3,531196
1
A: Phosphoenolpyruvate carboxykinase [ATP]


Theoretical massNumber of molelcules
Total (without water)58,7101
Polymers58,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoenolpyruvate carboxykinase [ATP]


Theoretical massNumber of molelcules
Total (without water)58,7101
Polymers58,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.659, 55.734, 139.397
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphoenolpyruvate carboxykinase [ATP] / PEP carboxykinase / Phosphoenolpyruvate carboxylase / PEPCK


Mass: 58709.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerobiospirillum succiniciproducens (bacteria)
Gene: pckA / Plasmid: pProEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha
References: UniProt: O09460, phosphoenolpyruvate carboxykinase (ATP)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG MME 5000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2004
Details: Diamond (111) double-crystal monochromator Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Diamond (111) double-crystal monochromator Bent cylindrical Si-mirror (Rh coating)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 43637 / Num. obs: 35963 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.067 / Net I/σ(I): 8.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3980 / Rsym value: 0.394 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→10 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 1810 RANDOM
Rwork0.221 --
all0.219 38295 -
obs0.219 35963 -
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7621 0 0 196 7817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.05
X-RAY DIFFRACTIONc_angle_deg8
X-RAY DIFFRACTIONc_dihedral_angle_d60
X-RAY DIFFRACTIONc_improper_angle_d3

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