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- PDB-7w61: Crystal structure of farnesol dehydrogenase from Helicoverpa armigera -

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Basic information

Entry
Database: PDB / ID: 7w61
TitleCrystal structure of farnesol dehydrogenase from Helicoverpa armigera
ComponentsFarnesol dehydrogenase
KeywordsOXIDOREDUCTASE / short chain dehydrogenase
Function / homologyACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesHelicoverpa armigera (cotton bollworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKumar, R. / Das, J. / Mahto, J.K. / Sharma, M. / Kumar, P. / Sharma, A.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2022
Title: Crystal structure and molecular characterization of NADP + -farnesol dehydrogenase from cotton bollworm, Helicoverpaarmigera.
Authors: Kumar, R. / Das, J. / Mahto, J.K. / Sharma, M. / Vivek, S. / Kumar, P. / Sharma, A.K.
History
DepositionDec 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5879
Polymers26,4241
Non-polymers1,1638
Water5,513306
1
A: Farnesol dehydrogenase
hetero molecules

A: Farnesol dehydrogenase
hetero molecules

A: Farnesol dehydrogenase
hetero molecules

A: Farnesol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,34836
Polymers105,6974
Non-polymers4,65132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area24460 Å2
ΔGint-122 kcal/mol
Surface area30940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.016, 118.016, 118.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Farnesol dehydrogenase


Mass: 26424.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicoverpa armigera (cotton bollworm) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2(DE3)

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Non-polymers , 6 types, 314 molecules

#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→29.52 Å / Num. obs: 36084 / % possible obs: 100 % / Redundancy: 26.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 24.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 1742 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XG5

1xg5


Resolution: 1.6→29.52 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.887 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 1790 5 %RANDOM
Rwork0.168 ---
obs0.1693 34027 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.23 Å2 / Biso mean: 12.022 Å2 / Biso min: 3.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 75 307 2231
Biso mean--13.36 26.07 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0121976
X-RAY DIFFRACTIONr_angle_refined_deg2.3341.6382693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06623.07778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43115320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.18159
X-RAY DIFFRACTIONr_chiral_restr0.1580.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021447
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 167 -
Rwork0.197 2461 -
all-2628 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.0548 Å / Origin y: -2.0509 Å / Origin z: 43.6799 Å
111213212223313233
T0.0045 Å20.0028 Å20.0056 Å2-0.021 Å20.0025 Å2--0.012 Å2
L0.1947 °2-0.0311 °20.0193 °2-0.0945 °2-0.0581 °2--0.0644 °2
S-0.0013 Å °0.0511 Å °-0.0016 Å °0.0048 Å °-0.0033 Å °0.0012 Å °0.0044 Å °0.0161 Å °0.0046 Å °

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