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- PDB-1kbl: PYRUVATE PHOSPHATE DIKINASE -

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Basic information

Entry
Database: PDB / ID: 1kbl
TitlePYRUVATE PHOSPHATE DIKINASE
ComponentsPYRUVATE PHOSPHATE DIKINASE
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / 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
AMMONIUM ION / Pyruvate, phosphate dikinase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsHerzberg, O. / Chen, C.C. / Liu, S.
Citation
Journal: Biochemistry / Year: 2002
Title: Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis
Authors: Herzberg, O. / Chen, C.C. / Liu, S. / Tempczyk, A. / Howard, A. / Wei, M. / Ye, D. / 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.
#2: Journal: Biochemistry / Year: 1998
Title: Location of the Phosphate Binding Site within Clostridium Symbiosum Pyruvate Phosphate Dikinase
Authors: Mcguire, M. / Huang, K. / Kapadia, G. / Herzberg, O. / Dunaway-Mariano, D.
#3: Journal: J.Biol.Chem. / Year: 2000
Title: Identification of Domain-Domain Docking Sites within Clostridium Symbiosum Pyruvate Phosphate Dikinase by Amino Acid Replacement
Authors: Wei, M. / Li, Z. / Ye, D. / Herzberg, O. / Dunaway-Mariano, D.
History
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)97,1397
Polymers96,6401
Non-polymers4986
Water15,835879
1
A: PYRUVATE PHOSPHATE DIKINASE
hetero molecules

A: PYRUVATE PHOSPHATE DIKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,27714
Polymers193,2802
Non-polymers99712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4060 Å2
ΔGint-146 kcal/mol
Surface area67630 Å2
MethodPISA
2
A: PYRUVATE PHOSPHATE DIKINASE
hetero molecules

A: PYRUVATE PHOSPHATE DIKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,27714
Polymers193,2802
Non-polymers99712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)89.837, 58.838, 102.949
Angle α, β, γ (deg.)90.00, 94.839, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-904-

SO4

21A-904-

SO4

DetailsA dimer generated by a crystallographic 2-fold axis: -1.0 0.0 0.0 89.837 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 0.0

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Components

#1: Protein PYRUVATE PHOSPHATE DIKINASE / PPDK


Mass: 96640.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: PPDK / Plasmid: PACYC184-D12 / Gene (production host): PPDK / Production host: Escherichia coli (E. coli) / Strain (production host): JM 101 / References: UniProt: P22983, pyruvate, phosphate dikinase
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / 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: 2.81 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50-54% saturated ammonium sulfate, 10 mg/ml protein solution in 100mM KCl and 20mM imidazole buffer (pH 6.5), 100 mM Hepes buffer (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃
Details: Herzberg, O., (1996) Proc.Natl.Acad.Sci.USA, 93, 2652.
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.3 / Wavelength: 1.3 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 1995
RadiationMonochromator: toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 79262 / Num. obs: 79262 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 23.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6736 / % possible all: 80.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 80.1 % / Num. unique obs: 6736 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PPDK + phosphonopyruvate (PDB entry 1KC7)

1kc7


Resolution: 1.94→20 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 2.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4390 5.5 %RANDOM
Rwork0.195 ---
all0.2064 75531 --
obs0.2008 72384 90.9 %-
Displacement parametersBiso mean: 37.9 Å2
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6752 0 26 879 7657
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.021
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.91
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 67245 / Num. reflection Rfree: 5139 / % reflection Rfree: 6.5 % / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.223
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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