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- PDB-2ahb: X-ray crystal structure of R46A,R161A mutant of Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 2ahb
TitleX-ray crystal structure of R46A,R161A mutant of Mycobacterium tuberculosis FabH
ComponentsBeta- ketoacyl-ACP synthase III
KeywordsTRANSFERASE / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III / BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III / mtFabH / FabH
Function / homology
Function and homology information


mycobacterial beta-ketoacyl-[acyl carrier protein] synthase III / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / long-chain fatty-acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / fatty-acyl-CoA binding / fatty acid elongation / secondary metabolite biosynthetic process / lipid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity ...mycobacterial beta-ketoacyl-[acyl carrier protein] synthase III / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / long-chain fatty-acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / fatty-acyl-CoA binding / fatty acid elongation / secondary metabolite biosynthetic process / lipid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 3 / Mycobacterial beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrown, A.K. / Sridharan, S. / Kremer, L. / Lindenberg, S. / Dover, L.G. / Sacchettini, J.C. / Besra, G.S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Probing the Mechanism of the Mycobacterium tuberculosis {beta}-Ketoacyl-Acyl Carrier Protein Synthase III mtFabH: FACTORS INFLUENCING CATALYSIS AND SUBSTRATE SPECIFICITY
Authors: Brown, A.K. / Sridharan, S. / Kremer, L. / Lindenberg, S. / Dover, L.G. / Sacchettini, J.C. / Besra, G.S.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all ..._reflns_shell.number_unique_all / _reflns_shell.percent_possible_all / _software.classification / _software.name
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta- ketoacyl-ACP synthase III
B: Beta- ketoacyl-ACP synthase III


Theoretical massNumber of molelcules
Total (without water)73,9332
Polymers73,9332
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-41 kcal/mol
Surface area22700 Å2
MethodPISA
2
A: Beta- ketoacyl-ACP synthase III
B: Beta- ketoacyl-ACP synthase III

A: Beta- ketoacyl-ACP synthase III
B: Beta- ketoacyl-ACP synthase III


Theoretical massNumber of molelcules
Total (without water)147,8674
Polymers147,8674
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area13740 Å2
ΔGint-94 kcal/mol
Surface area43770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.445, 81.412, 97.281
Angle α, β, γ (deg.)90.00, 106.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

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Components

#1: Protein Beta- ketoacyl-ACP synthase III / 3-oxoacyl-[acyl-carrier-protein] synthase III / KAS III / MtFabH


Mass: 36966.641 Da / Num. of mol.: 2 / Mutation: R46A, R161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fabH / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3)
References: UniProt: P0A574, UniProt: P9WNG3*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.75 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7.5
Details: 0.1 M HEPES, 10% v/v isopropanol, 20% w/v PEG 4000, pH 7.5, microbatch under oil , temperature 291.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 52336 / Num. obs: 51995 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Limit h min: -51 / Limit k max: 40 / Limit k min: -51 / Limit l max: 48 / Limit l min: 0 / Observed criterion F max: 1960952.97 / Observed criterion F min: 4
Reflection shellResolution: 2→2.1 Å / Num. unique all: 6835

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Processing

Software
NameVersionClassification
ADVXdata collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
Adxvdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M1M

1m1m


Resolution: 2→40 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.248 2654 random
Rwork0.218 --
all0.949 51995 -
obs-51973 -
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 53.6137 Å2 / ksol: 0.37771 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å2-5.42 Å2
2--2.08 Å20 Å2
3----1.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 0 237 5097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.98

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