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

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Basic information

Entry
Database: PDB / ID: 4ttp
TitleCrystal structure of Legionella pneumophila dephospho-CoA kinase in apo-form
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 / ATP binding / cytoplasm
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dephospho-CoA kinase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGong, X. / Ge, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270770 China
Ministry of Science and Technology (MoST, China)2012CB917200 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 1.3Oct 11, 2017Group: 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 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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


Theoretical massNumber of molelcules
Total (without water)24,6341
Polymers24,6341
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.229, 72.330, 96.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 52.8 %
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: 12960 / % possible obs: 96.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.2 / % possible all: 97.9

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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→33.898 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 639 4.94 %
Rwork0.188 --
obs0.1896 12938 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→33.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 0 91 1700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041648
X-RAY DIFFRACTIONf_angle_d0.6992231
X-RAY DIFFRACTIONf_dihedral_angle_d15.613636
X-RAY DIFFRACTIONf_chiral_restr0.03264
X-RAY DIFFRACTIONf_plane_restr0.003281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.36970.2251380.2092431X-RAY DIFFRACTION98
2.3697-2.60810.24581240.20192471X-RAY DIFFRACTION98
2.6081-2.98520.23781310.19832442X-RAY DIFFRACTION97
2.9852-3.76030.23161200.18142458X-RAY DIFFRACTION96
3.7603-33.9020.19481260.17752497X-RAY DIFFRACTION93

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