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- PDB-1xdp: Crystal Structure of the E.coli Polyphosphate Kinase in complex w... -

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Basic information

Entry
Database: PDB / ID: 1xdp
TitleCrystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP
ComponentsPolyphosphate kinase
KeywordsTRANSFERASE / E.coli polyphosphate kinase / PPK / PPK complex with AMPPNP / AMPPNP
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
ADENOSINE-5'-TRIPHOSPHATE / Polyphosphate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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: Polyphosphate kinase
B: Polyphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,9408
Polymers160,8282
Non-polymers1,1126
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-40 kcal/mol
Surface area56860 Å2
MethodPISA
2
A: Polyphosphate kinase
B: Polyphosphate kinase
hetero molecules

A: Polyphosphate kinase
B: Polyphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,88016
Polymers321,6574
Non-polymers2,22312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area17820 Å2
ΔGint-98 kcal/mol
Surface area107560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.000, 152.000, 150.000
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 / / 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) / Strain (production host): BL21star
References: UniProt: P0A7B1, ATP-polyphosphate phosphotransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1,6 Hexanediol, Hepes, DTT, Magnesium chloride, AMPPNP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97939, 0.95372
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979391
30.953721
ReflectionResolution: 2.5→20 Å / Num. all: 121657 / Num. obs: 113237 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.56 Å / % possible all: 87

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / σ(F): 0
RfactorNum. reflection
Rfree0.274 1802
Rwork0.248 -
obs0.337 105842
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.038 Å20 Å20 Å2
2---2.038 Å20 Å2
3---4.076 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11342 0 66 130 11538
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.0081
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_deg1.45
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_it1.4371.5
X-RAY DIFFRACTIONo_mcangle_it2.5822
X-RAY DIFFRACTIONo_scbond_it1.712
X-RAY DIFFRACTIONo_scangle_it2.7642.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.rep.param
X-RAY DIFFRACTION2water.param

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