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- PDB-3af4: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -

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Basic information

Entry
Database: PDB / ID: 3af4
TitlePantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with GMPPCP
ComponentsPantothenate kinase
KeywordsTRANSFERASE / Homodimer / COA biosynthesis / Nucleotide binding / ATP-binding / Kinase / Nucleotide-binding
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Pantothenate kinase / Pantothenate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChetnani, B. / Kumar, P. / Surolia, A. / Vijayan, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: M. tuberculosis pantothenate kinase: dual substrate specificity and unusual changes in ligand locations
Authors: Chetnani, B. / Kumar, P. / Surolia, A. / Vijayan, M.
History
DepositionFeb 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,42315
Polymers35,7051
Non-polymers1,71814
Water2,972165
1
A: Pantothenate kinase
hetero molecules

A: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,84730
Polymers71,4102
Non-polymers3,43728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3890 Å2
ΔGint-32 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.400, 103.400, 91.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Pantothenate kinase / / MtPanK / Pantothenic acid kinase


Mass: 35704.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: coaA, Rv1092c / Plasmid: pET-28a(+) (NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4-1.8M trisodium citrate, 0.05-0.1M sodium acetate, 10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 22, 2009 / Details: Mirrors
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 17745 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 66.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2696 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GEV

2gev


Resolution: 2.6→34.23 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24774 875 4.9 %RANDOM
Rwork0.19882 ---
obs0.2012 16829 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.403 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20.8 Å20 Å2
2--1.6 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 110 165 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222639
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9963576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1035306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4422.126127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7415417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8411531
X-RAY DIFFRACTIONr_chiral_restr0.0920.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211980
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4691.51541
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7722498
X-RAY DIFFRACTIONr_scbond_it3.97131098
X-RAY DIFFRACTIONr_scangle_it6.4284.51078
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 60 -
Rwork0.31 1206 -
obs--100 %

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