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- PDB-1kc7: Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate -

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Basic information

Entry
Database: PDB / ID: 1kc7
TitlePyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate
Componentspyruvate phosphate dikinase
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / phosphonopyruvate inhibitor
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
PHOSPHONOPYRUVATE / Pyruvate, phosphate dikinase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsChen, C.C. / Howard, A. / Herzberg, O.
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.H. / 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 7, 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 / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)97,2177
Polymers96,6401
Non-polymers5776
Water00
1
A: pyruvate phosphate dikinase
hetero molecules

A: pyruvate phosphate dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,43314
Polymers193,2802
Non-polymers1,15312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4310 Å2
ΔGint-141 kcal/mol
Surface area66230 Å2
MethodPISA
2
A: pyruvate phosphate dikinase
hetero molecules

A: pyruvate phosphate dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,43314
Polymers193,2802
Non-polymers1,15312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)89.21, 58.42, 102.55
Angle α, β, γ (deg.)90.0, 94.99, 90.0
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-1003-

SO4

21A-1003-

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 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 101 / References: UniProt: P22983, pyruvate, phosphate dikinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PPR / PHOSPHONOPYRUVATE


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P

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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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 54% saturated ammonium sulfate, 100mM Hepes buffer (pH 7.0), 9mg/ml protein solution consisting of: 20mM imidazole buffer (pH 6.5), 100mM KCl, 40mM phosphonopyruvate, 5mM MgCl2, 0.1mM EDTA, ...Details: 54% saturated ammonium sulfate, 100mM Hepes buffer (pH 7.0), 9mg/ml protein solution consisting of: 20mM imidazole buffer (pH 6.5), 100mM KCl, 40mM phosphonopyruvate, 5mM MgCl2, 0.1mM EDTA, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
154 %satammonium sulfate1reservoir
2100 mMHEPES1reservoirpH7.0
39 mg/mlprotein1drop
420 mMimidazole1droppH6.5
5100 mM1dropKCl
640 mMphosphonopyruvate1drop
75 mM1dropMgCl2
80.1 mMEDTA1drop
91 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2001 / Details: mirror
RadiationMonochromator: CRYOGENITCALLY-COOLED SI(111) DOUBLE CRYSTAL system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→25 Å / Num. all: 104444 / Num. obs: 104444 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 26.6
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.1 / Num. unique all: 14814 / % possible all: 81.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 81.4 % / Num. unique obs: 14814 / Rmerge(I) obs: 0.523

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Processing

Software
NameVersionClassification
CNS0.9refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1DIK

1dik


Resolution: 2.2→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2584 -RANDOM
Rwork0.198 ---
all-52306 --
obs-51903 96.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6752 0 31 0 6783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.9
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Num. reflection obs: 49319 / σ(F): 2 / % reflection Rfree: 4.8 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.9

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