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- PDB-1dik: PYRUVATE PHOSPHATE DIKINASE -

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Basic information

Entry
Database: PDB / ID: 1dik
TitlePYRUVATE PHOSPHATE DIKINASE
ComponentsPYRUVATE PHOSPHATE DIKINASEPyruvate, phosphate dikinase
KeywordsPHOSPHOTRANSFERASE / TRANSFERASE / KINASE
Function / homology
Function and homology information


pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / kinase activity / phosphorylation / 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, B domain / ATP-grasp fold, subdomain 1 / 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 / Resolution: 2.3 Å
AuthorsHerzberg, O. / Chen, C.C.H.
CitationJournal: 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
DepositionDec 6, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRUVATE PHOSPHATE DIKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0744
Polymers96,7851
Non-polymers2883
Water7,494416
1
A: PYRUVATE PHOSPHATE DIKINASE
hetero molecules

A: PYRUVATE PHOSPHATE DIKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,1478
Polymers193,5712
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4770 Å2
ΔGint-75 kcal/mol
Surface area63080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.800, 58.800, 102.000
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-875-

SO4

21A-1005-

HOH

31A-1014-

HOH

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Components

#1: Protein PYRUVATE PHOSPHATE DIKINASE / Pyruvate, phosphate dikinase / PPDK


Mass: 96785.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PH7.0, CRYSTALLIZATION AT 30C, DATA COLLECTION AT ROOM TEMP
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: PPDK / Plasmid: PACYC184D-12 / Gene (production host): PPDK / Production host: Escherichia coli (E. coli) / Strain (production host): JM 101 / References: UniProt: P22983, pyruvate, phosphate dikinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 30 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMimidazole1drop
3100 mM1dropKCl
40.1 mMEDTA1drop
51 mM2-mercaptoethanol1drop
650-55 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 7, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.3 Å / Num. obs: 44378 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Rmerge(I) obs: 0.082

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.182 --
obs0.182 34662 80 %
Displacement parametersBiso mean: 27.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6730 0 15 416 7161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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