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- PDB-4i1u: Apo crystal structure of a dephospho-CoA kinase from Burkholderia... -

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Basic information

Entry
Database: PDB / ID: 4i1u
TitleApo crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis
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 / coenzyme A / biosynthesis / kinase / ATP-dependent
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
Dephospho-CoA kinase
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Apo crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis
Authors: Edwards, T.E. / Abendroth, J. / 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_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_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

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Assembly

Deposited unit
A: Dephospho-CoA kinase
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,95414
Polymers45,8962
Non-polymers1,05812
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-123 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.420, 116.420, 89.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-535-

HOH

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.83 Å3/Da / Density % sol: 67.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BuviA.00139.a.B1 PS01581 at 26.1 mg/mL against MCSG 1 screen condition G5, 2 M ammonium sulfate, 0.1 M BisTris pH 6.5, with 20% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: BuviA.00139.a.B1 PS01581 at 26.1 mg/mL against MCSG 1 screen condition G5, 2 M ammonium sulfate, 0.1 M BisTris pH 6.5, with 20% ethylene glycol as cryo-protectant, crystal tracking ID 236782g5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 28, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 44492 / Num. obs: 44198 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 34.916 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.10.4174.5719594319997.6
2.1-2.160.3646.2224623315399.6
2.16-2.220.3368.1831978305099.7
2.22-2.290.3089.0532284299899.3
2.29-2.370.25110.6431373288799.3
2.37-2.450.22711.2430342277698.8
2.45-2.540.18612.9929549270499.2
2.54-2.650.15914.4228761262499.4
2.65-2.760.14414.8927382248499.5
2.76-2.90.11717.3826707241899.7
2.9-3.060.09721.1425239227999.4
3.06-3.240.08125.5824075217599.9
3.24-3.470.05936.4422568204499.8
3.47-3.740.0543.5921040191099.9
3.74-4.10.04447.7919317175599.3
4.1-4.580.03855.5517428159299.5
4.58-5.290.03655.7715551142599.5
5.29-6.480.03950.08133211220100
6.48-9.170.02960.110223955100
9.170.02568.23541955098.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å43.98 Å
Translation3 Å43.98 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHL
Resolution: 2.05→44.02 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2066 / WRfactor Rwork: 0.1812 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8368 / SU B: 6.662 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1478 / SU Rfree: 0.1405 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 2234 5.1 %RANDOM
Rwork0.2012 ---
obs0.2028 44196 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.51 Å2 / Biso mean: 33.514 Å2 / Biso min: 16.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.22 Å2-0 Å2
2--0.22 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 55 296 3403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193219
X-RAY DIFFRACTIONr_bond_other_d0.0010.023115
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9674396
X-RAY DIFFRACTIONr_angle_other_deg0.8137082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28721.793145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20615499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7251543
X-RAY DIFFRACTIONr_chiral_restr0.0850.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 156 -
Rwork0.227 3033 -
all-3189 -
obs--97.46 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2530.333-0.26550.9967-0.07980.61310.0165-0.00710.00280.0366-0.0769-0.09810.0190.00380.06050.0252-0.01750.00250.05090.03130.085669.313328.6358-12.1601
21.16170.5920.03110.5066-0.01830.0067-0.0052-0.10790.065-0.05920.01070.09870.0129-0.0166-0.00550.0999-0.08570.00760.0861-0.00680.032479.470846.358811.8726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 202
2X-RAY DIFFRACTION2B0 - 201

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