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- PDB-2gp6: X-ray crystal structure of Mycobacterium tuberculosis beta-ketoac... -

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Basic information

Entry
Database: PDB / ID: 2gp6
TitleX-ray crystal structure of Mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase II (mtKasB)
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / thiolase fold / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / mycolic acid biosynthetic process / cell wall / fatty acid elongation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / response to hypoxia / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 2 / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSridharan, S. / Sacchettini, J. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: X-Ray Crystal Structure of Mycobacterium tuberculosis beta-Ketoacyl Acyl Carrier Protein Synthase II (mtKasB).
Authors: Sridharan, S. / Wang, L. / Brown, A.K. / Dover, L.G. / Kremer, L. / Besra, G.S. / Sacchettini, J.C.
History
DepositionApr 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2


Theoretical massNumber of molelcules
Total (without water)92,3022
Polymers92,3022
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-45 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.682, 198.682, 71.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-532-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 46151.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: kasB / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: P63456, UniProt: P9WQD7*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 100 mM CAPS pH 10.5, 20% PEG 8000, 100-150 mM NaCl, FOS-choline, Spermine-HCl, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 41266 / % possible obs: 98.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.053 / Χ2: 0.977 / Net I/σ(I): 19.2
Reflection shellResolution: 2.39→2.48 Å / % possible obs: 88.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.431 / Num. unique obs: 3696 / Χ2: 0.877

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT1.701data extraction
MAR345data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 980 / Stereochemistry target values: Engh & Huber
Details: Refined using twinned data set. Twin operator is h,-h-k,-l. Twin fraction is 0.41
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1911 4.6 %random
Rwork0.177 ---
all-37785 --
obs-37785 91.4 %-
Solvent computationBsol: 48.271 Å2
Displacement parametersBiso mean: 55.285 Å2
Baniso -1Baniso -2Baniso -3
1-4.135 Å2-1.842 Å20 Å2
2--4.135 Å20 Å2
3----8.27 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6192 0 0 229 6421
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071.5
X-RAY DIFFRACTIONc_angle_deg1.182
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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