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

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Basic information

Entry
Database: PDB / ID: 4ttr
TitleCrystal structure of Legionella pneumophila dephospho-CoA kinase in complex with Bu2
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
1,3-BUTANEDIOL / PHOSPHATE ION / Dephospho-CoA kinase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYu, D. / 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: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8193
Polymers24,6341
Non-polymers1852
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-6 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.290, 82.200, 81.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 0.23 M ammonium citrate dibasic, 17.5%(w/v) PEG 3350, 0.01 M ATP, 5%(v/v) 1,3-butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.1→22.76 Å / Num. obs: 12710 / % possible obs: 84.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 4.6 / % possible all: 82.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jjv

1jjv


Resolution: 2.1→22.721 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 651 5.13 %
Rwork0.188 --
obs0.19 12698 85.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→22.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 11 123 1735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041664
X-RAY DIFFRACTIONf_angle_d0.7642254
X-RAY DIFFRACTIONf_dihedral_angle_d14.629643
X-RAY DIFFRACTIONf_chiral_restr0.031266
X-RAY DIFFRACTIONf_plane_restr0.002283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.26220.26821060.21871960X-RAY DIFFRACTION83
2.2622-2.48960.2511360.20262460X-RAY DIFFRACTION90
2.4896-2.84920.27451340.20712371X-RAY DIFFRACTION86
2.8492-3.58750.22581660.18122639X-RAY DIFFRACTION94
3.5875-22.72250.18161090.17142617X-RAY DIFFRACTION87

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