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- PDB-1uzn: MabA from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1uzn
TitleMabA from Mycobacterium tuberculosis
Components3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE
KeywordsOXIDOREDUCTASE / BETA-KETOACYL REDUCTASE
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 / 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 ...: / : / 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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier-protein] reductase MabA / 3-oxoacyl-[acyl-carrier-protein] reductase MabA
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsCohen-Gonsaud, M. / Ducasse, S. / Quemard, A. / Labesse, G.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of Maba from Mycobacterium Tuberculosis, a Reductase Involved in Long-Chain Fatty Acid Biosynthesis.
Authors: Cohen-Gonsaud, M. / Ducasse, S. / Hoh, F. / Zerbib, D. / Labesse, G. / Quemard, A.
History
DepositionMar 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)52,7727
Polymers51,4972
Non-polymers1,2755
Water4,882271
1
A: 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE
B: 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE
hetero molecules

A: 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE
B: 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,54314
Polymers102,9934
Non-polymers2,55010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13210 Å2
ΔGint-452.1 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.539, 117.111, 51.869
Angle α, β, γ (deg.)90.00, 122.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE / REDUCTASE / 3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE


Mass: 25748.273 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q48930, UniProt: P9WGT3*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAINS A AND B CYS 60 TO VAL 60 ENGINEERED MUTATION IN CHAINS A AND B SER ...ENGINEERED MUTATION IN CHAINS A AND B CYS 60 TO VAL 60 ENGINEERED MUTATION IN CHAINS A AND B SER 144 TO LEU 144 CATALYTIC ACTIVITY: (3R)-3-HYDROXYACYL-[ACYL-CARRIER PROTEIN] + NADP(+) = 3-OXOACYL-[ACYL-CARRIER PROTEIN] + NADPH.

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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: 1.8 Å3/Da / Density % sol: 32 %
Crystal growpH: 6.6
Details: PIPES PH 6.6 CSCL 400 MM, PEG 3000 12%, NADP 100 MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 28001 / % possible obs: 93.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17
Reflection shellResolution: 1.91→1.96 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.3 / % possible all: 76.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.109 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1462 5 %RANDOM
Rwork0.185 ---
obs0.187 28001 92.9 %-
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: 21.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å22.79 Å2
2---2.38 Å20 Å2
3---3.55 Å2
Refinement stepCycle: LAST / Resolution: 1.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 34 271 3653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213431
X-RAY DIFFRACTIONr_bond_other_d0.0020.023179
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9554646
X-RAY DIFFRACTIONr_angle_other_deg0.78337327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6975462
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_restr0.0710.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023929
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02696
X-RAY DIFFRACTIONr_nbd_refined0.2050.2728
X-RAY DIFFRACTIONr_nbd_other0.2330.23671
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.22050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.6380.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4870.250
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.2128
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 67
Rwork0.253 1166
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)
10.9446-0.00220.89512.1115-0.0031.2802-0.0535-0.03760.36840.0226-0.1887-0.1494-0.0311-0.01910.24220.0642-0.00610.02140.14410.0130.16238.59410.327.889
21.92990.40950.84512.10880.57190.60940.32560.0737-0.15140.1606-0.1656-0.18020.25550.0593-0.15990.17920.0329-0.02480.14210.02120.04349.731-12.5776.222
316.0154-8.762-2.168136.086712.701316.7133-0.4198-0.55041.80951.1530.30350.6882-1.8425-1.11990.11630.58690.05670.16590.5955-0.14360.3926-7.0597.26223.549
42.12510.21830.48050.92990.1665-0.63110.0933-0.63440.20530.1814-0.47650.2482-0.0361-0.42010.38320.21520.00610.04440.3134-0.09020.315-1.42911.48210.47
53.0648-0.55812.00133.3031-1.20433.1397-0.1709-0.20220.60990.2679-0.1176-0.38-0.3131-0.00010.28840.123-0.05-0.03810.1371-0.00230.321818.01117.66215.655
63.82911.35671.60314.14290.41092.18680.5036-0.0617-0.69750.3714-0.1717-0.41220.42730.1232-0.33190.33190.0297-0.18540.16260.02270.214618.699-20.23914.815
743.669239.6929-30.806962.643710.28795.0325-1.1411.1391-0.16975.56692.20530.7675-0.8875-0.8225-1.06430.37330.0368-0.07770.5401-0.0730.42825.02919.56816.241
83.76051.27541.62146.25593.79256.4471-0.16940.50190.639-0.5759-0.0663-0.4655-0.66910.65640.23570.0961-0.07310.0840.25870.21940.46924.72916.9952.529
91.6951-1.05321.36132.8221-1.52830.43990.3211-0.4223-0.75120.76360.0153-0.10620.2908-0.1084-0.33630.6076-0.1474-0.11280.41460.08430.2917.57-19.4223.722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 86
2X-RAY DIFFRACTION1A101 - 123
3X-RAY DIFFRACTION1A132 - 137
4X-RAY DIFFRACTION1A151 - 173
5X-RAY DIFFRACTION1A178 - 188
6X-RAY DIFFRACTION1A207 - 245
7X-RAY DIFFRACTION2B79 - 86
8X-RAY DIFFRACTION2B101 - 123
9X-RAY DIFFRACTION2B132 - 137
10X-RAY DIFFRACTION2B151 - 173
11X-RAY DIFFRACTION2B178 - 245
12X-RAY DIFFRACTION3A189 - 206
13X-RAY DIFFRACTION4A87 - 93
14X-RAY DIFFRACTION4A138 - 142
15X-RAY DIFFRACTION4A143 - 150
16X-RAY DIFFRACTION5A9 - 73
17X-RAY DIFFRACTION6B9 - 73
18X-RAY DIFFRACTION7A1249
19X-RAY DIFFRACTION8A74 - 78
20X-RAY DIFFRACTION8A124 - 131
21X-RAY DIFFRACTION8A174 - 177
22X-RAY DIFFRACTION9B74 - 78
23X-RAY DIFFRACTION9B124 - 131
24X-RAY DIFFRACTION9B174 - 177

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