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- PDB-2h3g: Structure of the Type III Pantothenate Kinase (CoaX) from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 2h3g
TitleStructure of the Type III Pantothenate Kinase (CoaX) from Bacillus Anthracis
ComponentsBIOSYNTHETIC PROTEIN
KeywordsBIOSYNTHETIC PROTEIN / pantothenate kinase / bacillus anthracis / anthrax / type III pantothenate kinase / CoaX / CoaA / ASKHA
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Type III pantothenate kinase / Type III pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type III pantothenate kinase / Type III pantothenate kinase
Similarity search - Component
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsNicely, N.I.
CitationJournal: Biochemistry / Year: 2007
Title: Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 A Resolution: Implications for Coenzyme A-Dependent Redox Biology.
Authors: Nicely, N.I. / Parsonage, D. / Paige, C. / Newton, G.L. / Fahey, R.C. / Leonardi, R. / Jackowski, S. / Mallett, T.C. / Claiborne, A.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
X: BIOSYNTHETIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0202
Polymers29,9581
Non-polymers621
Water3,243180
1
X: BIOSYNTHETIC PROTEIN
hetero molecules

X: BIOSYNTHETIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0394
Polymers59,9152
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3760 Å2
ΔGint-13 kcal/mol
Surface area22420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.852, 133.396, 41.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11X-402-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by crystallographic symmetry and interacting mainly through residues 147-161 and 179-203.

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Components

#1: Protein BIOSYNTHETIC PROTEIN


Mass: 29957.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Ames / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q73FE2, UniProt: Q81VX4*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein buffer: 10 mM Na HEPES pH 7.5, 10 mM KCl protein concentration: 22.5-25.0 mg/mL reservoir solution: 24-26% ethylene glycol reservoir volume: 0.5 mL drop volume: 2 + 2 uL or 4 + 4 uL, ...Details: protein buffer: 10 mM Na HEPES pH 7.5, 10 mM KCl protein concentration: 22.5-25.0 mg/mL reservoir solution: 24-26% ethylene glycol reservoir volume: 0.5 mL drop volume: 2 + 2 uL or 4 + 4 uL, protein + reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9798, 0.9800, 0.9500
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 27, 2006
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.981
30.951
Reflection

Av σ(I) over netI: 14.9 / Number: 161979 / Rmerge(I) obs: 0.05 / Χ2: 0.82 / D res high: 2.1 Å / D res low: 44.53 Å / Num. obs: 22637 / % possible obs: 99.9 / Redundancy: 7.1 %

ID
1
2
3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancyRejects
4.5244.5310010.0391.016.45310
3.594.5299.710.0350.726.93296
3.143.5999.510.0430.87.07242
2.853.1499.610.0650.827.18150
2.652.8510010.0920.847.16143
2.492.6510010.1240.927.2252
2.372.4910010.1610.877.2716
2.262.3710010.2030.827.276
2.182.2610010.260.747.25
2.12.1810010.2890.697.29
4.5244.5310020.0391.016.45310
3.594.5299.720.0350.726.93296
3.143.5999.520.0430.87.07242
2.853.1499.620.0650.827.18150
2.652.8510020.0920.847.16143
2.492.6510020.1240.927.2252
2.372.4910020.1610.877.2716
2.262.3710020.2030.827.276
2.182.2610020.260.747.25
2.12.1810020.2890.697.29
4.5244.5310030.0391.016.45310
3.594.5299.730.0350.726.93296
3.143.5999.530.0430.87.07242
2.853.1499.630.0650.827.18150
2.652.8510030.0920.847.16143
2.492.6510030.1240.927.2252
2.372.4910030.1610.877.2716
2.262.3710030.2030.827.276
2.182.2610030.260.747.25
2.12.1810030.2890.697.29
ReflectionResolution: 2→44.47 Å / Num. all: 26073 / Num. obs: 26073 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Phasing

Phasing dmFOM : 0.62 / FOM acentric: 0.61 / FOM centric: 0.63 / Reflection: 26036 / Reflection acentric: 22710 / Reflection centric: 3326
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-31.1150.960.970.941223842381
3.6-5.70.960.970.9335612924637
2.9-3.60.890.90.8343813784597
2.5-2.90.730.740.6543653862503
2.1-2.50.450.470.3577246947777
2-2.10.180.190.1347824351431

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.06phasing
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→35.18 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.8 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1324 5.1 %RANDOM
Rwork0.215 ---
all0.217 26073 --
obs0.217 24696 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.916 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 4 180 2104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221978
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9792675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26724.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53115361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.411158
X-RAY DIFFRACTIONr_chiral_restr0.110.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021451
X-RAY DIFFRACTIONr_nbd_refined0.2160.2908
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.215
X-RAY DIFFRACTIONr_mcbond_it1.451.51275
X-RAY DIFFRACTIONr_mcangle_it2.06921999
X-RAY DIFFRACTIONr_scbond_it3.0893811
X-RAY DIFFRACTIONr_scangle_it4.6214.5674
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 88 -
Rwork0.246 1822 -
obs-1910 100 %

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