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- PDB-1u6e: 1.85 Angstrom Crystal Structure of the C112A Mutant of Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 1u6e
Title1.85 Angstrom Crystal Structure of the C112A Mutant of Mycobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Synthase III (FabH)
Components3-oxoacyl-[acyl-carrier-protein] synthase III
KeywordsTRANSFERASE / 3-oxoacyl-[acyl-carrier-protein] synthase III
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
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: 1.85 Å
AuthorsMussayev, F. / Sachedeva, 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 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 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 1.4Aug 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)69,8846
Polymers69,7432
Non-polymers1424
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-85 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.263, 109.021, 110.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B

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
11ALAALAASNASNAA10 - 1920 - 29
21ALAALAASNASNBB10 - 1920 - 29
32GLUGLUTHRTHRAA21 - 3531 - 45
42GLUGLUTHRTHRBB21 - 3531 - 45
53THRTHRILEILEAA37 - 3947 - 49
63THRTHRILEILEBB37 - 3947 - 49
74THRTHRLEULEUAA41 - 6351 - 73
84THRTHRLEULEUBB41 - 6351 - 73
95ASNASNLEULEUAA65 - 10875 - 118
105ASNASNLEULEUBB65 - 10875 - 118
116ALAALAASPASPAA110 - 150120 - 160
126ALAALAASPASPBB110 - 150120 - 160
137GLYGLYGLYGLYAA152 - 183162 - 193
147GLYGLYGLYGLYBB152 - 183162 - 193
158GLNGLNALAALAAA185 - 285195 - 300
168GLNGLNALAALABB185 - 285195 - 300
179LEULEUMETMETAA287 - 317302 - 332
189LEULEUMETMETBB287 - 317302 - 332

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.19 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M NaCl, 100mM potassium/sodium phosphate 100 mM sodium Mes 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 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 25, 2002 / 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: 1.85→27 Å / Num. all: 58002 / Num. obs: 56576 / % possible obs: 97.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 0.044 / Net I/σ(I): 9.1
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5 / Rsym value: 0.135 / % possible all: 0.82

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1HZP

1hzp


Resolution: 1.85→26.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.604 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS with residues 1-3172 in each monomer comprising a TLS group
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Used simulated annealing in cns followed by maximum likelihood refinement with TLS on refmac
RfactorNum. reflection% reflectionSelection details
Rfree0.20571 5743 10.2 %RANDOM
Rwork0.18021 ---
obs0.18277 50770 97.48 %-
all-58002 --
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: 13.013 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.72 Å20 Å2
3----0.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.233 Å
Refinement stepCycle: LAST / Resolution: 1.85→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 4 556 5422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214990
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.956795
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5615676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023846
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.22510
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2462
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4061.53329
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77925297
X-RAY DIFFRACTIONr_scbond_it1.27731661
X-RAY DIFFRACTIONr_scangle_it2.0894.51498
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2213 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.150.5
medium thermal0.462
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 338
Rwork0.205 3041
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)
10.32320.1313-0.16040.4412-0.09520.4119-0.0047-0.0242-0.0167-0.0165-0.0075-0.00230.04960.02760.01220.0010.0022-0.0060.0416-0.00450.038421.329513.99770.4449
20.336-0.0175-0.08120.4912-0.00320.431-0.0182-0.0015-0.0544-0.0636-0.00390.02070.146-0.01630.02210.091-0.0118-0.0010.05090.00690.061511.3032-13.91380.3619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-10 - 3171 - 332
2X-RAY DIFFRACTION2BB-10 - 3171 - 332

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