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- PDB-4fw8: Crystal structure of FABG4 complexed with Coenzyme NADH -

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Basic information

Entry
Database: PDB / ID: 4fw8
TitleCrystal structure of FABG4 complexed with Coenzyme NADH
Components3-oxoacyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / short-chain dehydrogenase/reductase
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 (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-ZPG / 3-oxoacyl-(Acyl-carrier-protein) reductase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsDutta, D. / Bhattacharyya, S. / Das, A.K.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal structure of hexanoyl-CoA bound to beta-ketoacyl reductase FabG4 of Mycobacterium tuberculosis
Authors: Dutta, D. / Bhattacharyya, S. / Roychowdhury, A. / Biswas, R. / Das, A.K.
History
DepositionJun 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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) reductase
B: 3-oxoacyl-(Acyl-carrier-protein) reductase
C: 3-oxoacyl-(Acyl-carrier-protein) reductase
D: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,5989
Polymers187,5124
Non-polymers3,0865
Water3,891216
1
A: 3-oxoacyl-(Acyl-carrier-protein) reductase
B: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5115
Polymers93,7562
Non-polymers1,7553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-46 kcal/mol
Surface area29870 Å2
MethodPISA
2
C: 3-oxoacyl-(Acyl-carrier-protein) reductase
D: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0874
Polymers93,7562
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-36 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.333, 71.304, 93.293
Angle α, β, γ (deg.)104.990, 97.080, 93.660
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 46878.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: O53665, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-ZPG / (2S,5R,8R,11S,14S,17S,21R)-5,8,11,14,17-PENTAMETHYL-4,7,10,13,16,19-HEXAOXADOCOSANE-2,21-DIOL


Mass: 424.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.14 Å3/Da / Density % sol: 42.6 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES PH 6.5, 47% (v/v) POLYPROPYLENE GLYCOL P400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.786→89.166 Å / Num. all: 37439 / Num. obs: 37439 / % possible obs: 96.2 % / Redundancy: 3.9 % / Rsym value: 0.113 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.79-2.943.80.5840.5031.51919450510.2950.5840.503389.1
2.94-3.1240.3920.342.32080152220.1970.3920.344.496.4
3.12-3.3340.2810.2433.21946248950.1410.2810.2435.897
3.33-3.640.1710.1485.21820245750.0860.1710.1489.197.3
3.6-3.9440.1270.10971691242560.0630.1270.10911.897.8
3.94-4.4140.090.0789.81514738130.0450.090.07815.698
4.41-5.0940.0750.06511.71346933950.0380.0750.06518.398.5
5.09-6.2340.0830.07210.51142128910.0420.0830.07216.598.9
6.23-8.813.90.0590.05113.7872922250.030.0590.05122.299.3
8.81-19.8583.90.0380.03219.3432011160.0190.0380.03231.990.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→19.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2093 / WRfactor Rwork: 0.142 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8409 / SU B: 34.677 / SU ML: 0.305 / SU R Cruickshank DPI: 0.3052 / SU Rfree: 0.4043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1889 5 %RANDOM
Rwork0.1618 ---
obs0.1656 37439 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 40.963 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å2-0.97 Å2-2.66 Å2
2--1.21 Å20.33 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.79→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12057 0 189 216 12462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212435
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.99216938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43651665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84823.878459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.446151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4561591
X-RAY DIFFRACTIONr_chiral_restr0.0940.22023
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219323
X-RAY DIFFRACTIONr_mcbond_it0.5221.58251
X-RAY DIFFRACTIONr_mcangle_it1213066
X-RAY DIFFRACTIONr_scbond_it1.58334184
X-RAY DIFFRACTIONr_scangle_it2.7454.53872
LS refinement shellResolution: 2.786→2.859 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 117 -
Rwork0.283 2248 -
all-2365 -
obs--82.06 %
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)
10.57020.05180.03610.53910.05841.05840.014-0.119-0.00250.02370.0245-0.01010.0653-0.204-0.03850.0304-0.01250.01660.09050.02670.07631.6399-0.16821.0727
20.57610.0115-0.24630.61660.12151.098-0.00710.04680.0747-0.01020.0258-0.047-0.18360.2513-0.01870.0631-0.05440.00760.08770.01590.066625.278216.4538-12.7687
31.2952-0.09370.6861.00590.09550.94770.0050.08080.07240.05190.0521-0.1256-0.0020.0274-0.05710.02730.02670.01350.05710.00140.0522-16.0348-25.532830.4816
41.23350.04980.59790.87210.21480.73840.133-0.0497-0.19430.2530.0269-0.06850.3163-0.1074-0.15990.2684-0.0102-0.10210.03330.0040.0584-20.9897-55.310342.217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 454
2X-RAY DIFFRACTION2B20 - 454
3X-RAY DIFFRACTION3C29 - 454
4X-RAY DIFFRACTION4D29 - 454

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