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- PDB-1jde: K22A mutant of pyruvate, phosphate dikinase -

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Basic information

Entry
Database: PDB / ID: 1jde
TitleK22A mutant of pyruvate, phosphate dikinase
ComponentsPYRUVATE, PHOSPHATE DIKINASE
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / nucleotide binding site mutant
Function / homology
Function and homology information


pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / kinase activity / ATP binding / metal ion binding
Similarity search - Function
Pyruvate Phosphate di-kinase; domain 2 / Pyruvate Phosphate Dikinase, domain 2 / Acyl-CoA Binding Protein - #30 / Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site ...Pyruvate Phosphate di-kinase; domain 2 / Pyruvate Phosphate Dikinase, domain 2 / Acyl-CoA Binding Protein - #30 / Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Acyl-CoA Binding Protein / Phosphoenolpyruvate-binding domains / Glucose Oxidase; domain 1 / ATP-grasp fold, A domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 3-Layer(bba) Sandwich / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pyruvate, phosphate dikinase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsYe, D. / Wei, M. / McGuire, M. / Huang, K. / Kapadia, G. / Herzberg, O. / Martin, B.M. / Dunaway-Mariano, D.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Investigation of the catalytic site within the ATP-grasp domain of Clostridium symbiosum pyruvate phosphate dikinase.
Authors: Ye, D. / Wei, M. / McGuire, M. / Huang, K. / Kapadia, G. / Herzberg, O. / Martin, B.M. / Dunaway-Mariano, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Swiveling-domain Mechanism for Enzymatic Phosphotransfer between Remote Reaction Sites
Authors: Herzberg, O. / Chen, C.C. / Kapadia, G. / McGuire, M. / Carroll, L.J. / Noh, S.J. / Dunaway-Mariano, D.
History
DepositionJun 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRUVATE, PHOSPHATE DIKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7743
Polymers96,5821
Non-polymers1922
Water73941
1
A: PYRUVATE, PHOSPHATE DIKINASE
hetero molecules

A: PYRUVATE, PHOSPHATE DIKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,5486
Polymers193,1642
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2650 Å2
ΔGint-80 kcal/mol
Surface area66810 Å2
MethodPISA
2
A: PYRUVATE, PHOSPHATE DIKINASE
hetero molecules

A: PYRUVATE, PHOSPHATE DIKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,5486
Polymers193,1642
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)89.9, 58.6, 102.3
Angle α, β, γ (deg.)90., 95.1, 90.
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-901-

SO4

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Components

#1: Protein PYRUVATE, PHOSPHATE DIKINASE / PPDK


Mass: 96582.047 Da / Num. of mol.: 1 / Mutation: K22A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: PODK / Plasmid: PACYC184D-12 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 101 / References: UniProt: P22983, pyruvate, phosphate dikinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50% saturated ammonium sulfate, 100mM Hepes buffer, 100mM KCL, 0.1mM EDTA, 1mM Mercaptoethanol, 20mM imidazole buffer pH 6.5, 10mg/ml protein, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150-55 %satammonium sulfate1reservoir
2100 mMHEPES1reservoirpH7.0
310 mg/mlprotein1drop
420 mMimidazole1droppH6.5
5100 mM1dropKCl
60.1 mMEDTA1drop
71 mMmercaptoethanol1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 5, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 25068 / Num. obs: 25068 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.8→2.9 Å / % possible all: 53

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1DIK without solvent molecules and with K22 truncated to Gly

1dik


Resolution: 2.8→10 Å / σ(F): 2 / Details: TNT was also used for refinement. /
RfactorNum. reflection
Rwork0.193 -
obs-20093
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6717 0 10 41 6768
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.7
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_plane_restr0.019

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