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- PDB-7djs: Crystal structure of isopiperitenol dehydrogenase from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 7djs
TitleCrystal structure of isopiperitenol dehydrogenase from Pseudomonas aeruginosa complexed with NAD
ComponentsSDR family oxidoreductase
KeywordsOXIDOREDUCTASE / complex / NAD
Function / homologyShort-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Short chain dehydrogenase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhan, J.R. / Zheng, Y.C.
CitationJournal: Adv.Synth.Catal. / Year: 2021
Title: Discovery and Engineering of Bacterial (-)-Isopiperitenol Dehydrogenases to Enhance (-)-Menthol Precursor Biosynthesis.
Authors: Zhan, J.R. / Shou, C. / Zheng, Y.C. / Chen, Q. / Pan, J. / Li, C.X. / Xu, J.H.
History
DepositionNov 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: 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: SDR family oxidoreductase
B: SDR family oxidoreductase
C: SDR family oxidoreductase
D: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9058
Polymers107,2514
Non-polymers2,6544
Water15,925884
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-132 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.201, 108.582, 124.609
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SDR family oxidoreductase / isopiperitenol dehydrogenase


Mass: 26812.752 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: DY930_09865, F7O90_18305, FDK04_18370, IPC116_19850, IPC36_02985
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A554HE32
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 100mM MES-imidazole pH 6.25, 30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 20% v/v PEG 500MME, 10% w/v PEG 20000
PH range: 6.25-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 100875 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.992 / Net I/σ(I): 27
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 5009 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X8H

5x8h


Resolution: 1.7→42.23 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 5011 4.98 %
Rwork0.1611 95693 -
obs0.1624 100704 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.54 Å2 / Biso mean: 16.0461 Å2 / Biso min: 2.97 Å2
Refinement stepCycle: final / Resolution: 1.7→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6836 0 176 884 7896
Biso mean--18.63 27.34 -
Num. residues----964
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.720.23711630.19743089325298
1.72-1.740.23551830.196531013284100
1.74-1.760.22691530.194632013354100
1.76-1.780.22731600.199131513311100
1.78-1.810.23221600.196231783338100
1.81-1.830.24341720.184731323304100
1.83-1.860.22221680.18131923360100
1.86-1.880.21041870.17531123299100
1.88-1.910.18121540.169631903344100
1.91-1.950.20091720.169531523324100
1.95-1.980.19061690.160331483317100
1.98-2.020.17511560.161131813337100
2.02-2.050.18541570.160731703327100
2.05-2.10.18511760.166131693345100
2.1-2.140.19341480.159131743322100
2.14-2.190.19521720.164431683340100
2.19-2.250.19111750.161331983373100
2.25-2.310.18911610.157431803341100
2.31-2.370.18561360.155332003336100
2.37-2.450.18471600.161731983358100
2.45-2.540.211940.158531673361100
2.54-2.640.2011790.16231703349100
2.64-2.760.20111620.163632163378100
2.76-2.910.18771660.163232183384100
2.91-3.090.18591620.156532293391100
3.09-3.330.15851710.156432133384100
3.33-3.660.15911730.151232353408100
3.66-4.190.14331920.141632443436100
4.19-5.280.16591520.138533093461100
5.28-42.230.19531780.1693408358699

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