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- PDB-1hzp: Crystal Structure of the Myobacterium Tuberculosis Beta-Ketoacyl-... -

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Basic information

Entry
Database: PDB / ID: 1hzp
TitleCrystal Structure of the Myobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Synthase III
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III
KeywordsTRANSFERASE / fatty acid biosynthesis / myobacterium tuberculosis / structural basis for substrate specificity / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 / 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
LAURIC ACID / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsScarsdale, J.N. / Kazanina, G. / He, X. / Reynolds, K.A. / Wright, H.T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III
Authors: Scarsdale, J.N. / Kazanina, G. / He, X. / Reynolds, K.A. / Wright, H.T.
History
DepositionJan 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 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

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Assembly

Deposited unit
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,65210
Polymers69,8072
Non-polymers8458
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-37 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.082, 54.779, 89.152
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III / MT-FABH


Mass: 34903.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P0A574, UniProt: P9WNG3*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.21 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: PEG4000, Tris/HCl. 300mM NaCl, glycerol, 10mM CaCl2, pH 8.0, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlenzyme1drop
250 mMTris-HCl1drop
3300 mM1dropNaCl
440 %glycerol1drop
52 mMdithiothreitol1drop
630 %PEG40001drop
7100 mMTris-HCl1drop
8300 mM1dropNaCl
910 mM1dropCaCl2
1017-26 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: Osmic Confocal optics
RadiationMonochromator: Osmic Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. all: 37716 / Num. obs: 37503 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1860 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameClassification
bioteXdata collection
SCALEPACKdata scaling
CNSrefinement
bioteXdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly alanine chain based on residues 1-317 from E Coli FabH (RCSB entry 1EBL)

1ebl


Resolution: 2.1→30.38 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 797513.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3560 10 %RANDOM
Rwork0.222 ---
obs0.222 35649 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.46 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.5 Å20 Å2-0.38 Å2
2--8.31 Å20 Å2
3----0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4743 0 56 258 5057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scbond_it7.452
X-RAY DIFFRACTIONc_scangle_it6.452.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 583 10 %
Rwork0.281 5257 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDAORYL.TOP
X-RAY DIFFRACTION3DAORYL.PARAMGOL.TOP
X-RAY DIFFRACTION4GOL.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_scbond_it7.452
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scangle_it6.452.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / % reflection Rfree: 10 % / Rfactor Rwork: 0.281 / Rfactor obs: 0.281

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