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- PDB-9pzl: Pyruvate phosphate dikinase in complex with AMP-PNP and sulfate ions -

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Basic information

Entry
Database: PDB / ID: 9pzl
TitlePyruvate phosphate dikinase in complex with AMP-PNP and sulfate ions
ComponentsPyruvate, phosphate dikinase
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / ATP-BINDING / PEP BINDING DIKINASE
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 dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding 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 ...Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding 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 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / ATP-grasp fold, subdomain 1
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pyruvate, phosphate dikinase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLim, K. / Herzberg, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB9813271 United States
CitationJournal: Biochemistry / Year: 2007
Title: Swiveling domain mechanism in pyruvate phosphate dikinase.
Authors: Lim, K. / Read, R.J. / Chen, C.C. / Tempczyk, A. / Wei, M. / Ye, D. / Wu, C. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate, phosphate dikinase
B: Pyruvate, phosphate dikinase
C: Pyruvate, phosphate dikinase
D: Pyruvate, phosphate dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,26320
Polymers387,0854
Non-polymers3,17816
Water00
1
A: Pyruvate, phosphate dikinase
B: Pyruvate, phosphate dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,13110
Polymers193,5432
Non-polymers1,5898
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-119 kcal/mol
Surface area63330 Å2
MethodPISA
2
C: Pyruvate, phosphate dikinase
D: Pyruvate, phosphate dikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,13110
Polymers193,5432
Non-polymers1,5898
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-116 kcal/mol
Surface area63800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.695, 118.475, 170.806
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvate, phosphate dikinase / Pyruvate / orthophosphate dikinase


Mass: 96771.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: ppdK / Production host: Escherichia coli (E. coli) / References: UniProt: P22983, pyruvate, phosphate dikinase
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PPDK 25mg/ml with 5mM MgCl2 + 5 mM AMPPNP in 2.3 M ammonium sulfate, 0.1 Na Hepes. Protein solution in 20 mM imidazole buffer, pH 6.5, 100 mM KCl, 0.1 mM EDTA and 1 mM mercaptoethanol
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 19, 2006
RadiationMonochromator: HARVARD MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→48 Å / Num. obs: 86567 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.06 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.208 / Num. unique obs: 4453 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
CrystalCleardata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.533 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.62 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3021 4374 5.08 %random selection
Rwork0.2187 ---
obs0.2245 86160 99.12 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.203 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.8351 Å20 Å2-0.4745 Å2
2--19.2285 Å2-0 Å2
3----10.3934 Å2
Refinement stepCycle: LAST / Resolution: 3→47.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27012 0 184 0 27196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127688
X-RAY DIFFRACTIONf_angle_d1.25237364
X-RAY DIFFRACTIONf_dihedral_angle_d18.24510408
X-RAY DIFFRACTIONf_chiral_restr0.0784076
X-RAY DIFFRACTIONf_plane_restr0.0054896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0005-3.05230.37372150.26814125X-RAY DIFFRACTION95
3.0523-3.10770.4062240.26194070X-RAY DIFFRACTION94
3.1077-3.16750.40382010.2614069X-RAY DIFFRACTION95
3.1675-3.23210.35042120.25334092X-RAY DIFFRACTION95
3.2321-3.30240.36922400.25544114X-RAY DIFFRACTION94
3.3024-3.37910.34072130.24134054X-RAY DIFFRACTION95
3.3791-3.46360.31982110.23824093X-RAY DIFFRACTION94
3.4636-3.55720.30261950.23064108X-RAY DIFFRACTION95
3.5572-3.66180.33532560.22774033X-RAY DIFFRACTION93
3.6618-3.77990.31361900.2214103X-RAY DIFFRACTION95
3.7799-3.91480.31252310.21464086X-RAY DIFFRACTION94
3.9148-4.07140.31912120.20614056X-RAY DIFFRACTION94
4.0714-4.25650.27752110.20084089X-RAY DIFFRACTION94
4.2565-4.48060.27152120.18894100X-RAY DIFFRACTION94
4.4806-4.76080.25832240.19114069X-RAY DIFFRACTION94
4.7608-5.12760.2412070.19784112X-RAY DIFFRACTION94
5.1276-5.64220.29282200.2194103X-RAY DIFFRACTION94
5.6422-6.45530.30172140.23424097X-RAY DIFFRACTION94
6.4553-8.12040.27312160.21464095X-RAY DIFFRACTION93
8.1204-38.47970.24032180.20014115X-RAY DIFFRACTION92

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