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- PDB-5ovj: Structure of the apo form of Mycobacterium smegmatis MabA -

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Basic information

Entry
Database: PDB / ID: 5ovj
TitleStructure of the apo form of Mycobacterium smegmatis MabA
Components3-oxoacyl-[acyl-carrier-protein] reductase FabG
KeywordsOXIDOREDUCTASE / FabG / beta-keto-reductase / FAS II
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / NADP binding / extracellular region
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 MabA
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKussau, T. / Van Wyk, N. / Viljoen, A. / Olieric, V. / Flipo, M. / Kremer, L. / Blaise, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structural rearrangements occurring upon cofactor binding in the Mycobacterium smegmatis beta-ketoacyl-acyl carrier protein reductase MabA.
Authors: Kussau, T. / Flipo, M. / Van Wyk, N. / Viljoen, A. / Olieric, V. / Kremer, L. / Blaise, M.
History
DepositionAug 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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 FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1319
Polymers53,4592
Non-polymers6727
Water6,738374
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)108,26218
Polymers106,9174
Non-polymers1,34514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area18440 Å2
ΔGint-271 kcal/mol
Surface area30690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.880, 68.270, 71.710
Angle α, β, γ (deg.)90.00, 123.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

21B-459-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta- ...3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta-ketoacyl-ACP reductase


Mass: 26729.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GMTVTDNPADTAGEATA part not seen in the electron density the first G belongs to the tag
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: fabG, MSMEG_3150, MSMEI_3069 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: P71534, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: BIS TRIS, DMSO, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→34.135 Å / Num. obs: 42269 / % possible obs: 98.75 % / Redundancy: 5 % / Rsym value: 0.13 / Net I/σ(I): 8.61
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 4171 / % possible all: 98.84

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OVL

5ovl


Resolution: 1.7→34.135 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2016 2000 4.73 %
Rwork0.1601 --
obs0.162 42254 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 35 374 3929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063596
X-RAY DIFFRACTIONf_angle_d0.7314852
X-RAY DIFFRACTIONf_dihedral_angle_d13.9122136
X-RAY DIFFRACTIONf_chiral_restr0.055540
X-RAY DIFFRACTIONf_plane_restr0.005644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.32091410.3132839X-RAY DIFFRACTION99
1.7425-1.78960.28041420.26392864X-RAY DIFFRACTION99
1.7896-1.84230.30671440.23362876X-RAY DIFFRACTION99
1.8423-1.90170.26081410.21682848X-RAY DIFFRACTION99
1.9017-1.96970.22981410.20692841X-RAY DIFFRACTION98
1.9697-2.04850.27011430.1772887X-RAY DIFFRACTION99
2.0485-2.14180.21521440.16552878X-RAY DIFFRACTION100
2.1418-2.25470.1971420.15612880X-RAY DIFFRACTION99
2.2547-2.39590.20271400.15512825X-RAY DIFFRACTION98
2.3959-2.58080.18341450.15422899X-RAY DIFFRACTION99
2.5808-2.84040.20661440.1482899X-RAY DIFFRACTION99
2.8404-3.25120.18981430.14352866X-RAY DIFFRACTION98
3.2512-4.0950.16041440.13022904X-RAY DIFFRACTION99
4.095-34.14190.17791460.14462948X-RAY DIFFRACTION99
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)
14.65270.0439-0.14384.5061-0.21310.0366-0.00310.01610.102-0.0444-0.0280.0677-0.09570.01220.02950.1495-0.0080.03030.13710.02950.1144-16.6694-2.913518.2933
24.9938-3.6419-2.1463.23343.12356.97190.39660.2901-0.1502-0.3632-0.26770.36580.0312-0.45280.00040.2655-0.0087-0.00960.1570.02960.1829-15.4234-2.37578.4267
32.0111-2.702-2.07356.46255.06576.03410.0540.08310.1005-0.4577-0.0242-0.3811-0.00680.1956-0.03570.2462-0.0190.03360.20190.05630.2145-5.7054-7.89455.5885
43.58624.0741.94484.86192.34041.1973-0.17610.26380.0931-0.45530.09080.1715-0.09640.0260.08290.27050.0004-0.02960.22610.02250.1963-18.0013-23.71547.6025
57.14815.02546.69777.33916.94438.49840.0080.2805-0.1994-0.17260.2116-0.5454-0.1350.4533-0.16430.154-0.00410.03660.17070.02870.1865-1.8743-14.059715.0854
60.32190.0878-0.12031.4971-0.24390.6511-0.040.04310.0211-0.09230.0159-0.0188-0.03650.03570.02610.16440.00910.00920.16910.00540.1569-14.0436-21.657920.1502
70.3425-0.1055-0.33061.4952-0.36950.93580.01330.1065-0.0207-0.19410.02580.22070.018-0.1477-0.03040.19110.0097-0.01450.16-0.00070.1619-26.5078-16.252921.2105
83.9095-0.06112.1495.79940.35964.0859-0.06330.026-0.0842-0.11290.0524-0.1690.11830.1560.0380.17260.02250.01390.1044-0.01240.0886-14.0827-54.251919.0501
96.26882.1537-3.67746.7363-5.41975.26650.0704-0.13-0.2327-0.3772-0.349-0.91460.39210.8850.39660.32540.01550.03740.2799-0.02770.2639-8.4784-55.128412.0771
104.07082.942-1.6828.4377-6.12256.8929-0.12750.25780.0087-0.68910.0636-0.13480.21540.00120.08190.32660.05190.02420.2037-0.03320.1812-12.9084-49.34122.36
114.33794.77290.01647.62720.31570.96830.07670.069-0.1999-0.0830.0154-0.51930.05080.232-0.11060.18190.04380.02550.1965-0.02150.1851-5.7065-33.616912.4264
128.10226.7951-3.72348.1357-2.77454.6158-0.1530.56790.3149-0.58530.24190.56440.2751-0.3268-0.10980.27130.0384-0.06830.1781-0.01450.1864-22.2421-43.14196.4825
133.89834.9063.16217.92843.21084.2167-0.16540.03450.0193-0.16850.0361-0.05810.0030.05180.13290.1010.03390.01890.1195-0.00080.1361-14.1613-37.22220.9009
140.2682-0.13220.13481.1607-0.03441.3548-0.00870.0093-0.007-0.02970.016-0.15450.01080.1547-0.00590.17610.00980.010.1745-0.01370.1884-11.9787-39.432625.43
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 121 )
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 255 )
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 45 )
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 87 )
11X-RAY DIFFRACTION11chain 'B' and (resid 88 through 121 )
12X-RAY DIFFRACTION12chain 'B' and (resid 122 through 138 )
13X-RAY DIFFRACTION13chain 'B' and (resid 139 through 158 )
14X-RAY DIFFRACTION14chain 'B' and (resid 159 through 255 )

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