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- PDB-1ggo: T453A MUTANT OF PYRUVATE, PHOSPHATE DIKINASE -

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Basic information

Entry
Database: PDB / ID: 1ggo
TitleT453A MUTANT OF PYRUVATE, PHOSPHATE DIKINASE
ComponentsPROTEIN (PYRUVATE, PHOSPHATE DIKINASE)
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE
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, 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 / OTHER / Resolution: 2.6 Å
AuthorsLi, Z. / Herzberg, O.
Citation
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.
#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
DepositionAug 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 1.4Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PROTEIN (PYRUVATE, PHOSPHATE DIKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8023
Polymers96,6101
Non-polymers1922
Water4,089227
1
A: PROTEIN (PYRUVATE, PHOSPHATE DIKINASE)
hetero molecules

A: PROTEIN (PYRUVATE, PHOSPHATE DIKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,6056
Polymers193,2202
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
2
A: PROTEIN (PYRUVATE, PHOSPHATE DIKINASE)
hetero molecules

A: PROTEIN (PYRUVATE, PHOSPHATE DIKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,6056
Polymers193,2202
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4860 Å2
ΔGint-83 kcal/mol
Surface area64650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.730, 58.660, 102.780
Angle α, β, γ (deg.)90.00, 95.58, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-1003-

HOH

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Components

#1: Protein PROTEIN (PYRUVATE, PHOSPHATE DIKINASE) / PPDK


Mass: 96610.125 Da / Num. of mol.: 1 / Mutation: T453A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Strain: JM 101 / 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


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.: 227 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 30 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150-55 %satammonium sulfate1reservoir
2100 mMHEPES1reservoir
310 mg/mlprotein1drop
420 mMimidazole1drop
5100 mM1dropKCl
60.1 mMEDTA1drop
71 mMmercaptoethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 15, 1999 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 27567 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.236 / % possible all: 68
Reflection
*PLUS
Num. measured all: 43302
Reflection shell
*PLUS
% possible obs: 68 %

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Processing

Software
NameVersionClassification
CNS0.4refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.6→50 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1016 5 %RANDOM
Rwork0.177 ---
obs0.177 21068 67 %-
Solvent computationBsol: 64 Å2 / ksol: 0.5 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 10 227 6964
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.7

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