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- PDB-2ntn: Crystal structure of MabA-C60V/G139A/S144L -

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Basic information

Entry
Database: PDB / ID: 2ntn
TitleCrystal structure of MabA-C60V/G139A/S144L
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / BETA-KETOACYL ACP REDUCTASE / inactive / SDR
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / short-chain fatty acid metabolic process / : / : / : / mycolic acid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / NADPH binding ...acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / short-chain fatty acid metabolic process / : / : / : / mycolic acid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / NADPH binding / extracellular region / plasma membrane
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
3-oxoacyl-[acyl-carrier-protein] reductase FabG1 / 3-oxoacyl-[acyl-carrier-protein] reductase MabA
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPoncet-Montange, G. / Ducasse-Cabanot, S. / Quemard, A. / Labesse, G. / Cohen-Gonsaud, M.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Lack of dynamics in the MabA active site kills the enzyme activity: practical consequences for drug-design studies
Authors: Poncet-Montange, G. / Ducasse-Cabanot, S. / Quemard, A. / Labesse, G. / Cohen-Gonsaud, M.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 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] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)55,8672
Polymers55,8672
Non-polymers00
Water4,306239
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase

A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)111,7354
Polymers111,7354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9680 Å2
ΔGint-62 kcal/mol
Surface area32500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.613, 117.285, 52.272
Angle α, β, γ (deg.)90.00, 121.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl Carrier Protein Reductase


Mass: 27933.670 Da / Num. of mol.: 2 / Mutation: C60V, G139A, S144L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37rv / Gene: fabG, fabG1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P0A5Y4, UniProt: P9WGT3*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 316 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG 2000, 0.35mM Mn acetate, 10% glycerol, 0.1M Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 316K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.3→26.54 Å / Num. all: 45213 / Num. obs: 17168 / Redundancy: 2.6 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3 / Num. unique all: 2563

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZM

1uzm


Resolution: 2.3→24 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.569 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23805 868 5.1 %RANDOM
Rwork0.17748 ---
obs0.18055 16293 92.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.541 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å2-0.91 Å2
2--0.06 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 0 239 3304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223103
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.9384190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01223.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76815491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6491525
X-RAY DIFFRACTIONr_chiral_restr0.0770.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022324
X-RAY DIFFRACTIONr_nbd_refined0.1890.21378
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.29
X-RAY DIFFRACTIONr_mcbond_it0.4311.52147
X-RAY DIFFRACTIONr_mcangle_it0.71923308
X-RAY DIFFRACTIONr_scbond_it1.08531058
X-RAY DIFFRACTIONr_scangle_it1.6964.5882
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 68 -
Rwork0.224 1216 -
obs--95.54 %
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)
13.04040.31771.15613.4764-1.09282.9299-0.1058-0.26560.38210.1652-0.0517-0.0138-0.4311-0.08960.1574-0.0817-0.0328-0.0305-0.0969-0.0259-0.089419.378618.736115.3738
21.0331-0.13871.16923.2103-0.57181.3772-0.0025-0.14280.09960.0727-0.03310.2472-0.1525-0.23340.0356-0.1151-0.00280.0022-0.05-0.0034-0.10947.868510.50788.9772
33.43551.48181.18564.1757-0.24152.31830.15150.0034-0.46530.1201-0.0904-0.34020.37120.1392-0.061-0.0950.0164-0.0419-0.10250.0488-0.062418.8599-21.216915.7429
41.65990.5070.67782.99740.55270.31880.13350.0886-0.2112-0.1197-0.062-0.04450.04360.042-0.0715-0.1016-0.0146-0.0108-0.06760.0149-0.09519.516-13.29817.1222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 8229 - 102
2X-RAY DIFFRACTION2AA83 - 245103 - 265
3X-RAY DIFFRACTION3BB9 - 8229 - 102
4X-RAY DIFFRACTION4BB83 - 245103 - 265

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