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- PDB-3q6i: Crystal structure of FabG4 and coenzyme binary complex -

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Basic information

Entry
Database: PDB / ID: 3q6i
TitleCrystal structure of FabG4 and coenzyme binary complex
Components3-oxoacyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / Ketoreductase / Cytosolic
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
NICOTINAMIDE-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: 2.59 Å
AuthorsDutta, D. / Bhattacharyya, S. / Das, A.K.
CitationJournal: To be Published
Title: Crystal structure of holoFabG4
Authors: Dutta, D. / Bhattacharyya, S. / Das, A.K.
History
DepositionJan 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)187,4829
Polymers184,4044
Non-polymers3,0785
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)93,9535
Polymers92,2022
Non-polymers1,7513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-28 kcal/mol
Surface area30530 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)93,5294
Polymers92,2022
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-27 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.069, 71.027, 92.917
Angle α, β, γ (deg.)105.020, 97.060, 93.660
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 46101.031 Da / Num. of mol.: 4 / Fragment: UNP residues 17-454
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#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: 2.15 Å3/Da / Density % sol: 42.86 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 47% Polypropylene glycol , 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
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.589→88.799 Å / Num. all: 45759 / Num. obs: 45759 / % possible obs: 95.4 % / Redundancy: 3.9 % / Rsym value: 0.151 / Net I/σ(I): 7.7
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
2.59-2.733.70.9790.8420.92391763940.4980.9790.8421.790.7
2.73-2.893.90.7270.6291.22486362980.3650.7270.6292.495.2
2.89-3.093.90.4560.3951.92350559570.2290.4560.3953.795.6
3.09-3.343.90.3080.2662.92189555510.1550.3080.2665.195.9
3.34-3.6640.1820.1574.82017751060.0910.1820.1578.196.5
3.66-4.0940.1280.1116.61859347030.0650.1280.11110.896.8
4.09-4.7340.0940.0818.91635041320.0470.0940.0811497.4
4.73-5.7940.0920.0798.91388035130.0460.0920.07914.297.7
5.79-8.193.90.0750.06510.71072727160.0380.0750.06516.398.1
8.19-19.77740.0480.04214549713890.0240.0480.04224.191.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.76 Å19.78 Å
Translation2.76 Å19.78 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LLS

3lls


Resolution: 2.59→19.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 1 / SU B: 28.312 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 2322 5.1 %RANDOM
Rwork0.1675 ---
obs0.1713 45758 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.28 Å2 / Biso mean: 42.729 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0.99 Å2-2.47 Å2
2--0.72 Å20.16 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.59→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12057 0 189 216 12462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212441
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9916946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68151666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97723.878459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.271151861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6261591
X-RAY DIFFRACTIONr_chiral_restr0.0980.22012
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219323
X-RAY DIFFRACTIONr_mcbond_it0.521.58256
X-RAY DIFFRACTIONr_mcangle_it0.965213074
X-RAY DIFFRACTIONr_scbond_it1.70134185
X-RAY DIFFRACTIONr_scangle_it2.7994.53872
LS refinement shellResolution: 2.589→2.656 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 147 -
Rwork0.241 2970 -
all-3117 -
obs--87.21 %
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)
11.3746-0.0287-0.07361.4878-0.00842.21630.0122-0.2429-0.02680.05770.05810.05350.1415-0.4211-0.07030.0221-0.02390.02040.13140.02960.05531.6143-0.15861.0553
21.3416-0.0224-0.15991.20110.04492.41390.00550.07160.2204-0.02930.0264-0.1381-0.40550.447-0.0320.079-0.08310.02710.12460.00350.105125.168116.4008-12.7235
31.8611-0.10280.72682.08710.19191.63310.01150.15560.2530.02410.0643-0.2903-0.07030.1155-0.07580.04230.03820.01750.1031-0.00690.103-15.963-25.455630.3527
42.19780.36880.85041.80290.40941.59440.2252-0.1608-0.47320.4940.032-0.14920.627-0.1511-0.25730.42580.007-0.13910.04180.0160.1304-20.8813-55.123342.0218
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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