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- PDB-2aj9: X-ray crystal structure of W42A,R161A double mutant of Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 2aj9
TitleX-ray crystal structure of W42A,R161A double mutant of Mycobacterium tuberculosis beta-ketoacyl-ACP synthase III
Components3-oxoacyl-[acyl-carrier-protein] synthase III
KeywordsTRANSFERASE / beta-ketoacyl-ACP synthase III / 3-oxoacyl-ACP 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: 2.5 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
DepositionAug 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 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 1.5Aug 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,8752
Polymers73,8752
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-41 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.174, 56.021, 88.190
Angle α, β, γ (deg.)90.00, 90.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36937.625 Da / Num. of mol.: 2 / Mutation: W42A, 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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.3 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7.5
Details: 0.2 M ammonium sulfate, 30 % w/v PEG 8000, pH 7.5, microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorDate: Nov 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 21850 / Num. obs: 21086 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 41.8 Å2 / Rsym value: 0.084 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.59 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
ADVXdata collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
Adxvdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1m1m

1m1m


Resolution: 2.5→28.01 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1980 9.8 %random
Rwork0.225 ---
all-21850 --
obs-20163 92 %-
Solvent computationSolvent model: CNS bulk solvent model / Bsol: 25.4257 Å2 / ksol: 0.302034 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.23 Å20 Å2-7.58 Å2
2--12.04 Å20 Å2
3----2.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 0 101 4955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.5→2.62 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.396 228 9.8 %
Rwork0.331 2097 -
obs--86.6 %

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