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- PDB-3v1t: Crystal structure of a putative ketoacyl reductase (FabG4) from M... -

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Basic information

Entry
Database: PDB / ID: 3v1t
TitleCrystal structure of a putative ketoacyl reductase (FabG4) from Mycobacterium tuberculosis H37Rv at 1.9 Angstrom resolution
Components3-oxoacyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / Ketoreductase / High Molecular Weight FabG (HMwFabG)
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
3-oxoacyl-(Acyl-carrier-protein) reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsDutta, D. / Bhattacharyya, S. / Das, A.K.
CitationJournal: To be Published
Title: Crystal structure of a putative ketoacyl reductase (FabG4) from Mycobacterium tuberculosis H37Rv at 1.9 Angstrom resolution
Authors: Dutta, D. / Bhattacharyya, S. / Das, A.K.
History
DepositionDec 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 3-oxoacyl-(Acyl-carrier-protein) reductase
D: 3-oxoacyl-(Acyl-carrier-protein) reductase


Theoretical massNumber of molelcules
Total (without water)95,7022
Polymers95,7022
Non-polymers00
Water11,962664
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-26 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.388, 57.594, 71.488
Angle α, β, γ (deg.)99.240, 102.980, 117.040
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: 47851.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fabG-1, fabG4, MT0256, Rv0242c / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: O53665, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / 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: 2.04 Å3/Da / Density % sol: 39.78 % / Mosaicity: 0 °
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 45%(v/v) polypropylene glycol, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 2, 2011
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.876→66.392 Å / Num. all: 56389 / Num. obs: 56389 / % possible obs: 91 % / Redundancy: 1.9 % / Rsym value: 0.057 / Net I/σ(I): 8
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
1.88-1.981.80.5270.3722.11226166660.3720.5270.3721.773.3
1.98-2.11.90.340.243.21472377880.240.340.242.791.2
2.1-2.241.90.2260.164.91406774190.160.2260.163.992.1
2.24-2.421.90.1650.1166.61327069810.1160.1650.1165.193.2
2.42-2.651.90.1190.0849.21233864670.0840.1190.0846.694.1
2.65-2.971.90.0840.0612.31129859210.060.0840.069.295
2.97-3.431.90.0560.0417.61006352790.040.0560.0413.395.7
3.43-4.21.90.0460.03219.5856444880.0320.0460.03217.896.7
4.2-5.931.90.0480.03417.6666234890.0340.0480.03419.397.5
5.93-19.6271.90.0470.03312.8360218910.0330.0470.03320.395.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMAC5.5.0095refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q6I

3q6i


Resolution: 1.88→66.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.623 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 2284 4.1 %RANDOM
Rwork0.1805 ---
obs0.1834 56360 90.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.49 Å2 / Biso mean: 26.298 Å2 / Biso min: 4.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å21.79 Å21.54 Å2
2--0.25 Å21.35 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.88→66.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5826 0 0 664 6490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225905
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9728034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34423.881219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91715885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2241543
X-RAY DIFFRACTIONr_chiral_restr0.1230.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214463
X-RAY DIFFRACTIONr_mcbond_it1.0821.54005
X-RAY DIFFRACTIONr_mcangle_it1.65326329
X-RAY DIFFRACTIONr_scbond_it2.88431900
X-RAY DIFFRACTIONr_scangle_it4.334.51705
LS refinement shellResolution: 1.876→1.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 101 -
Rwork0.252 2581 -
all-2682 -
obs--58.32 %
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)
10.8521-0.1065-0.37580.5984-0.16980.8406-0.00780.1927-0.0267-0.1322-0.01150.04250.0749-0.09330.01930.0697-0.0207-0.0230.0637-0.02110.04680.9154-0.3501-16.1898
20.8169-0.1881-0.35580.6678-0.17961.0333-0.0022-0.1973-0.03730.18230.02640.0221-0.02660.0923-0.02430.0962-0.0249-0.00830.0817-0.01650.0446-0.77570.220816.2639
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C29 - 454
2X-RAY DIFFRACTION2D29 - 454

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