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- PDB-1xdo: Crystal Structure of Escherichia coli Polyphosphate Kinase -

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Basic information

Entry
Database: PDB / ID: 1xdo
TitleCrystal Structure of Escherichia coli Polyphosphate Kinase
ComponentsPolyphosphate kinase
KeywordsTRANSFERASE / polyphosphate kinase / PPK / E.coli polyphosphate kinase
Function / homology
Function and homology information


diphosphotransferase activity / polyphosphate kinase complex / polyphosphate:AMP phosphotransferase activity / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / periplasmic side of cell outer membrane / phosphotransferase activity, phosphate group as acceptor / polyphosphate kinase activity / phosphorylation / protein homodimerization activity ...diphosphotransferase activity / polyphosphate kinase complex / polyphosphate:AMP phosphotransferase activity / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / periplasmic side of cell outer membrane / phosphotransferase activity, phosphate group as acceptor / polyphosphate kinase activity / phosphorylation / protein homodimerization activity / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Polyphosphate kinase N-terminal domain / polyphosphate kinase like / Polyphosphate kinase middle domain / Polyphosphate kinase / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase middle domain superfamily / Polyphosphate kinase N-terminal domain superfamily / Polyphosphate kinase, C-terminal domain 1 ...Polyphosphate kinase N-terminal domain / polyphosphate kinase like / Polyphosphate kinase middle domain / Polyphosphate kinase / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase middle domain superfamily / Polyphosphate kinase N-terminal domain superfamily / Polyphosphate kinase, C-terminal domain 1 / Polyphosphate kinase middle domain / Polyphosphate kinase N-terminal domain / Polyphosphate kinase C-terminal domain 2 / Polyphosphate kinase C-terminal domain 1 / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Endonuclease Chain A / Endonuclease; Chain A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyphosphate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhu, Y. / Huang, W. / Lee, S.S. / Xu, W.
CitationJournal: Embo Rep. / Year: 2005
Title: Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis
Authors: Zhu, Y. / Huang, W. / Lee, S.S. / Xu, W.
History
DepositionSep 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 19, 2014Group: Other
Revision 1.4Jul 28, 2021Group: Refinement description / Category: refine
Item: _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method
Revision 1.5Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyphosphate kinase
B: Polyphosphate kinase


Theoretical massNumber of molelcules
Total (without water)160,8282
Polymers160,8282
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-3 kcal/mol
Surface area60370 Å2
MethodPISA
2
A: Polyphosphate kinase
B: Polyphosphate kinase

A: Polyphosphate kinase
B: Polyphosphate kinase


Theoretical massNumber of molelcules
Total (without water)321,6574
Polymers321,6574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area12760 Å2
ΔGint-28 kcal/mol
Surface area114380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.000, 154.000, 155.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Polyphosphate kinase / / PPK / Polyphosphoric acid kinase / ATP- polyphosphate phosphotransferase


Mass: 80414.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ppk / Plasmid: pQE60 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A7B1, ATP-polyphosphate phosphotransferase

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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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1,6 Hexanediol, Hepes, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9729 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9729 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 37809 / % possible obs: 74.4 % / Observed criterion σ(F): 3.6 / Observed criterion σ(I): 3.6
Reflection shellResolution: 3→3.12 Å / % possible all: 74.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XDP

1xdp


Resolution: 3→20 Å / Cross valid method: FREE R-VALUE / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1007 3.1 %Random
Rwork0.255 ---
all0.274 33528 --
obs0.265 32521 97 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å20 Å2
2---1.88 Å23.759 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11234 0 0 0 11234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.009
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_deg1.42
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_it1.5561.5
X-RAY DIFFRACTIONo_mcangle_it2.8482
X-RAY DIFFRACTIONo_scbond_it1.6922
X-RAY DIFFRACTIONo_scangle_it2.8492.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

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