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- PDB-4i1v: Crystal structure of a dephospho-CoA kinase from Burkholderia vie... -

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Basic information

Entry
Database: PDB / ID: 4i1v
TitleCrystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis bound to ADP
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / National Institute for Allergy and Infectious Disease / ATP-dependent / ADP / CoA / COD
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
ADENOSINE-5'-DIPHOSPHATE / Dephospho-CoA kinase
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis bound to ADP
Authors: Edwards, T.E. / Clifton, M.C. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Dephospho-CoA kinase
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7514
Polymers45,8962
Non-polymers8542
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.860, 115.860, 91.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 0 - 200 / Label seq-ID: 8 - 208

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 22948.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (bacteria) / Strain: G4 / Gene: Bcep1808_0550, coaE / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A4JBA9, dephospho-CoA kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.87 Å3/Da / Density % sol: 68.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BuviA.00139.a.B1 PS01581 at 26.1 mg/mL with 2 mM ADP against Morpheus screen condition F1, 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each monosaccharide, 0.1 M MES/imidazole pH 6.5, crystal ...Details: BuviA.00139.a.B1 PS01581 at 26.1 mg/mL with 2 mM ADP against Morpheus screen condition F1, 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each monosaccharide, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 237917f1, unique puck ID beh5-16, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 22230 / Num. obs: 22169 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 59.114 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.6-2.670.53.78952162499.8
2.67-2.740.3864.88583156899.7
2.74-2.820.2986.268329153499.9
2.82-2.910.22988115149099.8
2.91-30.17910.027896145799.8
3-3.110.14612.317512139399.9
3.11-3.230.11515.017294136199.8
3.23-3.360.08219.656949131199.9
3.36-3.510.05826.676636126299.8
3.51-3.680.05527.936339120199.7
3.68-3.880.04533.745954114899.6
3.88-4.110.03739.045453107799.7
4.11-4.390.02947.375023101599.8
4.39-4.750.02651.98454693699.7
4.75-5.20.02552.9444988899.4
5.2-5.810.02650.31400181299.6
5.81-6.710.02551.84343371699.7
6.71-8.220.0264.993118614100
8.22-11.630.01575.74238248099.4
11.630.01576.29133128297.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å37.74 Å
Translation3 Å37.74 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4i1u

4i1u


Resolution: 2.6→44.04 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2267 / WRfactor Rwork: 0.198 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8237 / SU B: 18.635 / SU ML: 0.196 / SU R Cruickshank DPI: 0.3336 / SU Rfree: 0.2547 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1130 5.1 %RANDOM
Rwork0.2128 ---
obs0.2148 22169 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.51 Å2 / Biso mean: 63.8381 Å2 / Biso min: 30.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.69 Å2-0 Å2
2--0.69 Å2-0 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 54 53 3070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193067
X-RAY DIFFRACTIONr_bond_other_d0.0040.022885
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.974203
X-RAY DIFFRACTIONr_angle_other_deg0.95436543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44223.065124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11715426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7081528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213553
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02693
Refine LS restraints NCS

Ens-ID: 1 / Number: 10592 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 76 -
Rwork0.332 1538 -
all-1614 -
obs--99.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63870.76980.16282.4356-0.2221.30410.1582-0.02920.14080.041-0.5481-0.05910.06850.17770.38990.1746-0.0380.04720.24860.04940.225268.445328.4372-13.5203
21.53091.50690.08461.59070.00290.0875-0.179-0.14820.1325-0.35510.02540.02980.0855-0.11340.15350.3053-0.22110.07560.24-0.1340.232778.997747.118412.2161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 202
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B0 - 201
4X-RAY DIFFRACTION2B301

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