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- PDB-1u6s: Crystal Structure of the Complex Between Mycobacterium Tuberculos... -

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Basic information

Entry
Database: PDB / ID: 1u6s
TitleCrystal Structure of the Complex Between Mycobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Synthase III and Lauroyl Coenzyme A
Components3-oxoacyl-[acyl-carrier-protein] synthase III
KeywordsTRANSFERASE / fatty acid biosynthesis / mycobacterium tuberculosis / substrate complex
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
DODECYL-COA / 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: 2.3 Å
AuthorsMusayev, F. / Sachdeva, S. / Scarsdale, J.N. / Reynolds, K.A. / Wright, H.T.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a substrate complex of Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III (FabH) with lauroyl-coenzyme A.
Authors: Musayev, F. / Sachdeva, S. / Scarsdale, J.N. / Reynolds, K.A. / Wright, H.T.
#1: Journal: 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
DepositionJul 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)71,6424
Polymers69,7432
Non-polymers1,9002
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-80 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.570, 63.190, 55.330
Angle α, β, γ (deg.)113.25, 100.82, 92.66
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALACYSCYSAA10 - 2320 - 33
21ALAALACYSCYSBB10 - 2320 - 33
32HISHISARGARGAA25 - 4235 - 52
42HISHISARGARGBB25 - 4235 - 52
53PHEPHEALAALAAA44 - 18654 - 196
63PHEPHEALAALABB44 - 18654 - 196
74ALAALAGLNGLNAA188 - 200198 - 210
84ALAALAGLNGLNBB188 - 200198 - 210
95PROPROLEULEUAA202 - 207212 - 221
105PROPROLEULEUBB202 - 207212 - 221
116GLYGLYPHEPHEAA209 - 213223 - 227
126GLYGLYPHEPHEBB209 - 213223 - 227
137TRPTRPMETMETAA215 - 228229 - 242
147TRPTRPMETMETBB215 - 228229 - 242
DetailsThe biological assembly is the dimer contained in the assymetric unit

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Components

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


Mass: 34871.324 Da / Num. of mol.: 2 / Mutation: C112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fabH / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P0A574, UniProt: P9WNG3*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-DCC / DODECYL-COA


Mass: 949.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H58N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.39 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium formate, 100 mM Na Hepes buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 23, 2003 / 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: 2.3→57.7 Å / Num. all: 29907 / Num. obs: 28396 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.9 / % possible all: 89.5

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Processing

Software
NameVersionClassification
bioteXdata collection
REFMAC5.1.24refinement
bioteXdata reduction
bioteXdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HZP

1hzp


Resolution: 2.3→57.74 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.454 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS with each monomer comprising a separate TLS group
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.452 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: structure was refined initially with CNS 1.0, followed by refinement with refmac 5.1.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1431 5 %RANDOM
Rwork0.20624 ---
obs0.20828 26965 94.95 %-
all-29907 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.65 Å2-0.02 Å2
2--1.3 Å21.68 Å2
3---0.48 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.3→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 122 193 5172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215104
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9786954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7795670
X-RAY DIFFRACTIONr_chiral_restr0.1320.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023879
X-RAY DIFFRACTIONr_nbd_refined0.2070.22643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.26
X-RAY DIFFRACTIONr_mcbond_it0.3761.53317
X-RAY DIFFRACTIONr_mcangle_it0.6925278
X-RAY DIFFRACTIONr_scbond_it0.94831787
X-RAY DIFFRACTIONr_scangle_it1.6884.51676
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1556 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.110.5
medium thermal0.252
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.412 96
Rwork0.333 1885
obs-1885
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9739-0.1707-0.10480.81880.06510.4058-0.01710.0287-0.1058-0.03720.02270.03810.0205-0.0157-0.00560.0263-0.0203-0.00530.05480.02590.02890.2585-11.9935-7.6912
20.8872-0.1609-0.09390.86620.08330.5050.0139-0.05530.06210.10840.00120.0055-0.08370.007-0.01520.0865-0.0223-0.01490.06420.02090.01780.657912.5379.1579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 319
2X-RAY DIFFRACTION2B1 - 319

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