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- PDB-3m1l: Crystal structure of a C-terminal trunacted mutant of a putative ... -

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Basic information

Entry
Database: PDB / ID: 3m1l
TitleCrystal structure of a C-terminal trunacted mutant of a putative ketoacyl reductase (FabG4) from Mycobacterium tuberculosis H37Rv at 2.5 Angstrom resolution
Components3-oxoacyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / Short chain dehydrogenase / ketoacyl reductase / Rossmann fold
Function / homology
Function and homology information


long-chain fatty-acyl-CoA metabolic process / short-chain fatty acid metabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / peptidoglycan-based cell wall / response to antibiotic / nucleotide binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3-oxoacyl-(Acyl-carrier-protein) reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsDutta, D. / Bhattacharyya, S. / Saha, B. / Das, A.K.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structure of FabG4 from Mycobacterium tuberculosis reveals the importance of C-terminal residues in ketoreductase activity
Authors: Dutta, D. / Bhattacharyya, S. / Mukherjee, S. / Saha, B. / Das, A.K.
History
DepositionMar 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Sep 16, 2020Group: Derived calculations / Structure summary / Category: struct / struct_site
Item: _struct.title / _struct_site.pdbx_auth_asym_id ..._struct.title / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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) reductase
B: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1723
Polymers89,1132
Non-polymers591
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-23 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.076, 80.497, 153.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-oxoacyl-(Acyl-carrier-protein) reductase / Putative ketoacyl reductase / PROBABLE 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE FABG4 (3-KETOACYL- ...Putative ketoacyl reductase / PROBABLE 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE FABG4 (3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE)


Mass: 44556.344 Da / Num. of mol.: 2 / Fragment: UNP residues 17-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0242c / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4)
References: UniProt: O53665, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Sodium Acetate, 15% (w/v) PEG3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 20, 2010 / Details: VARIMAX MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.52→19.95 Å / Num. obs: 27834 / Redundancy: 7 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.1
Reflection shellHighest resolution: 2.52 Å / Redundancy: 6 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7827

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0095refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→19.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.904 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1138 4.1 %RANDOM
Rwork0.181 ---
obs0.183 27784 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.66 Å2 / Biso mean: 37.792 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2--1.73 Å20 Å2
3----3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.52→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5258 0 4 207 5469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225361
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9717286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73123.366202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33515822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2811543
X-RAY DIFFRACTIONr_chiral_restr0.1020.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214035
X-RAY DIFFRACTIONr_mcbond_it0.7781.53582
X-RAY DIFFRACTIONr_mcangle_it1.49525686
X-RAY DIFFRACTIONr_scbond_it2.39931779
X-RAY DIFFRACTIONr_scangle_it4.1134.51600
LS refinement shellResolution: 2.519→2.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 80 -
Rwork0.262 1736 -
all-1816 -
obs--89.63 %
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)
11.6955-0.13420.64341.2903-0.46441.9804-0.1280.05070.2035-0.09160.0963-0.0465-0.00990.08580.03170.0916-0.01240.00240.0231-0.01810.073346.697676.5588.1905
21.79980.15581.00140.7718-0.16532.60080.0267-0.2020.12210.19570.01440.05620.0047-0.1827-0.04110.14440.00890.00590.0262-0.00780.070143.701169.774643.086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 447
2X-RAY DIFFRACTION2B33 - 447

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