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- PDB-1jjv: DEPHOSPHO-COA KINASE IN COMPLEX WITH ATP -

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Basic information

Entry
Database: PDB / ID: 1jjv
TitleDEPHOSPHO-COA KINASE IN COMPLEX WITH ATP
ComponentsDEPHOSPHO-COA KINASE
KeywordsTRANSFERASE / P-loop nucleotide-binding fold / Structure 2 Function Project / S2F / Structural Genomics
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Dephospho-CoA kinase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsObmolova, G. / Teplyakov, A. / Bonander, N. / Eisenstein, E. / Howard, A.J. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: J.Struct.Biol. / Year: 2001
Title: Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae.
Authors: Obmolova, G. / Teplyakov, A. / Bonander, N. / Eisenstein, E. / Howard, A.J. / Gilliland, G.L.
History
DepositionJul 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: DEPHOSPHO-COA KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1164
Polymers23,3131
Non-polymers8043
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.000, 45.900, 41.700
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DEPHOSPHO-COA KINASE / / DEPHOSPHOCOENZYME A KINASE


Mass: 23312.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: YacE / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P44920, dephospho-CoA kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.58 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, PEG 400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 7 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19 mg/mlprotein1drop
22 Mammonium sulfate1drop
35 %(w/v)PEG4001drop
450 mM1dropNaCl
55 mMMMC1drop
61 mMdithiothreitol1drop
710 mMATP1drop
820 mMHEPES1droppH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9999 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 17, 2001
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 15767 / Num. obs: 15767 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.057 / Net I/σ(I): 37.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 7.5 / Rsym value: 0.121 / % possible all: 83
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / % possible obs: 97.6 % / Num. measured all: 56478 / Rmerge(I) obs: 0.057

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2→10 Å / SU B: 3.6 / SU ML: 0.1 / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.218 800 random
Rwork0.165 --
all0.168 14850 -
obs0.168 14850 -
Refine analyze
FreeObs
Luzzati coordinate error0.154 Å0.162 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 37 207 1788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d1.788
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.2
X-RAY DIFFRACTIONp_mcangle_it7.8
X-RAY DIFFRACTIONp_scbond_it10.8
X-RAY DIFFRACTIONp_scangle_it13.7
X-RAY DIFFRACTIONp_plane_restr0.008
X-RAY DIFFRACTIONp_chiral_restr0.122
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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