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- PDB-2dik: R337A MUTANT OF PYRUVATE PHOSPHATE DIKINASE -

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Basic information

Entry
Database: PDB / ID: 2dik
TitleR337A 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, K. / Herzberg, O.
Citation
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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Swiveling-Domain Mechanism for Enzymatic Phosphotransfer between Remote Reaction Sites
Authors: Herzberg, O. / Cheng, C.C.H. / Kapadia, G. / Mcguire, M. / Carroll, L.J. / Noh, S.J. / Dunaway-Mariano, D.
History
DepositionSep 3, 1998Deposition site: BNL / Processing site: RCSB
SupersessionSep 13, 1999ID: 1BUK
Revision 1.0Sep 13, 1999Provider: 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 1.4Nov 3, 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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PYRUVATE PHOSPHATE DIKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7603
Polymers96,5681
Non-polymers1922
Water79344
1
A: PROTEIN (PYRUVATE PHOSPHATE DIKINASE)
hetero molecules

A: PROTEIN (PYRUVATE PHOSPHATE DIKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,5206
Polymers193,1362
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2560 Å2
ΔGint-63 kcal/mol
Surface area64850 Å2
MethodPISA
2
A: PROTEIN (PYRUVATE PHOSPHATE DIKINASE)
hetero molecules

A: PROTEIN (PYRUVATE PHOSPHATE DIKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,5206
Polymers193,1362
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)89.800, 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-901-

SO4

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Components

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


Mass: 96568.055 Da / Num. of mol.: 1 / Mutation: R337A
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 44 / 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 / pH: 7 / Details: pH 7.0, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃ / pH: 6.5 / 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
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. obs: 35455 / % possible obs: 95 % / Observed criterion σ(I): 1.2 / Redundancy: 2.8 % / Rsym value: 9.9
Reflection shellResolution: 2.5→2.66 Å / % possible all: 83
Reflection
*PLUS
% possible obs: 95 % / Num. measured all: 97563 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 83 % / Mean I/σ(I) obs: 1.2

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Processing

Software
NameClassification
TNTrefinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DIK

1dik


Resolution: 2.5→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.185 --
obs-26796 75 %
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 10 44 6778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.79
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 3 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.79

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