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- PDB-3tqc: Structure of the pantothenate kinase (coaA) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tqc
TitleStructure of the pantothenate kinase (coaA) from Coxiella burnetii
ComponentsPantothenate kinase
KeywordsTRANSFERASE / Biosynthesis of cofactors / prosthetic groups / carriers
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / 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 / Pantothenate kinase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFranklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 13, 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_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: Pantothenate kinase
B: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3324
Polymers74,4772
Non-polymers8542
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-38 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.214, 94.698, 75.398
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEHOHHOHAA - E10 - 32013
21ILEILEHOHHOHBB - F10 - 32013
12ADPADPADPADPAC500
22ADPADPADPADPBD500

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Components

#1: Protein Pantothenate kinase / Pantothenic acid kinase


Mass: 37238.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_0199, coaA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83EV9, pantothenate 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.: 390 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.2 M sodium chloride, 10% PEG8000, 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 51888 / Num. obs: 46728 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.062 / Net I/σ(I): 22.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 2552 / Rsym value: 0.306 / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1ESM

1esm


Resolution: 2.3→72.33 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 13.799 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26861 1802 5.1 %RANDOM
Rwork0.2109 ---
obs0.21381 35570 93.68 %-
all-37970 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.956 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.34 Å2
2---1.9 Å20 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.3→72.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4994 0 54 390 5438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225170
X-RAY DIFFRACTIONr_bond_other_d0.0010.023512
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9687025
X-RAY DIFFRACTIONr_angle_other_deg0.83138561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5915604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68324.033243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87715909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3991530
X-RAY DIFFRACTIONr_chiral_restr0.070.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021061
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4531.53039
X-RAY DIFFRACTIONr_mcbond_other0.1031.51213
X-RAY DIFFRACTIONr_mcangle_it0.88224956
X-RAY DIFFRACTIONr_scbond_it1.54132131
X-RAY DIFFRACTIONr_scangle_it2.514.52069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4263 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.37 Å

TypeWeight position
MEDIUM POSITIONAL0.5
MEDIUM THERMAL2
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 137 -
Rwork0.242 2409 -
obs--90.38 %
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)
11.59150.1707-0.00351.9008-0.38371.38880.0309-0.1233-0.27670.0966-0.0156-0.07410.22510.064-0.01530.0510.0108-0.01650.01760.01570.0674-2.26490.3959-24.8353
21.660.25760.05361.90210.3181.27610.034-0.15120.25060.1267-0.00810.0928-0.2143-0.0471-0.02580.06220.01310.00550.0249-0.00960.065-7.762833.9547-24.2681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 318
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2B10 - 318
4X-RAY DIFFRACTION2B500

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