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- PDB-4ttq: Crystal structure of Legionella pneumophila dephospho-CoA kinase ... -

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Basic information

Entry
Database: PDB / ID: 4ttq
TitleCrystal structure of Legionella pneumophila dephospho-CoA kinase in complex with ATP
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / Kinase / P-loop / Coenzyme metabolism
Function / homology
Function and homology information


dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Dephospho-CoA kinase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, X. / Ge, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270770 China
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystal structure of Legionella pneumophila dephospho-CoA kinase reveals a non-canonical conformation of P-loop.
Authors: Gong, X. / Chen, X. / Yu, D. / Zhang, N. / Zhu, Z. / Niu, L. / Mao, Y. / Ge, H.
History
DepositionJun 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Oct 7, 2015Group: Experimental preparation
Revision 1.3Jan 8, 2020Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3314
Polymers24,6341
Non-polymers6973
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-15 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.369, 36.210, 82.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

21A-424-

HOH

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Components

#1: Protein Dephospho-CoA kinase / / Dephosphocoenzyme A kinase


Mass: 24633.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: coaE, lpg1467 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Rosetta / References: UniProt: Q5ZVH3, dephospho-CoA kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Sodium citrate (pH 5.6), 12%(w/v) PEG4000, 18%(v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12675 / % possible obs: 96.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.5 / % possible all: 94.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TTR

4ttr


Resolution: 2.2→33.148 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 619 4.89 %
Rwork0.1894 --
obs0.1924 12663 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→33.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 41 56 1699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151687
X-RAY DIFFRACTIONf_angle_d1.6112290
X-RAY DIFFRACTIONf_dihedral_angle_d17.371648
X-RAY DIFFRACTIONf_chiral_restr0.061266
X-RAY DIFFRACTIONf_plane_restr0.008282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.41670.37411360.24922949X-RAY DIFFRACTION96
2.4167-2.76620.31991740.22252980X-RAY DIFFRACTION98
2.7662-3.48460.2331500.1843015X-RAY DIFFRACTION97

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