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- PDB-7vr4: Crystal structure of (-)-pulegone reductase PR1294 from Nepeta te... -

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Basic information

Entry
Database: PDB / ID: 7vr4
TitleCrystal structure of (-)-pulegone reductase PR1294 from Nepeta tenuifolia in complex with NADPH
Components(-)-pulegone reductase PR1294 from Nepeta tenuifolia in complex with NADPH
KeywordsPLANT PROTEIN / double bond reductase
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesSchizonepeta tenuifolia (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsLin, W. / Wang, W.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of (-)-pulegone reductase PR1294 from Nepeta tenuifolia in complex with NADPH
Authors: Lin, W. / Wang, W.W.
History
DepositionOct 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 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: (-)-pulegone reductase PR1294 from Nepeta tenuifolia in complex with NADPH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9942
Polymers38,2511
Non-polymers7431
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-6 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.245, 71.199, 81.146
Angle α, β, γ (deg.)90.000, 101.580, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein (-)-pulegone reductase PR1294 from Nepeta tenuifolia in complex with NADPH


Mass: 38250.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizonepeta tenuifolia (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris (pH 6.5), 25 % W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.69→19.63 Å / Num. obs: 80816 / % possible obs: 96.53 % / Redundancy: 6.5 % / CC1/2: 0.997 / Net I/σ(I): 16.4
Reflection shellResolution: 1.69→1.75 Å / Num. unique obs: 3348 / CC1/2: 0.977 / % possible all: 79.07

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EQL

7eql


Resolution: 1.69→19.628 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 20.55 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.1962 2000 4.84 %
Rwork0.1617 76905 -
obs0.1633 80816 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.95 Å2 / Biso mean: 29.4989 Å2 / Biso min: 12.42 Å2
Refinement stepCycle: final / Resolution: 1.69→19.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 48 290 2966
Biso mean--17.59 37.59 -
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6902-1.71080.4061610.3591127645
1.7108-1.73250.26041200.2665239984
1.7325-1.75520.23551410.2399270896
1.7552-1.77930.21981420.2276279298
1.7793-1.80470.25951420.2115279598
1.8047-1.83160.2411460.2067285698
1.8316-1.86020.2231330.2054271799
1.8602-1.89070.26131460.2011289299
1.8907-1.92320.25611390.2034274299
1.9232-1.95820.2331460.1928284399
1.9582-1.99580.19651430.1881279999
1.9958-2.03650.19421440.1868283699
2.0365-2.08070.20861430.1817280799
2.0807-2.12910.2141400.1794283799
2.1291-2.18230.19411410.1807274999
2.1823-2.24120.20921500.1753289699
2.2412-2.3070.17331440.1801277999
2.307-2.38140.16881430.1741280199
2.3814-2.46630.19461480.1714287499
2.4663-2.56490.18621410.17382799100
2.5649-2.68130.22891460.16442828100
2.6813-2.82230.20821450.16432819100
2.8223-2.99860.23521400.15892850100
2.9986-3.22920.16251470.15342856100
3.2292-3.55240.18281450.14112853100
3.5524-4.06250.20191440.13292829100
4.0625-5.10330.14981430.11282841100
5.1033-19.6280.18181480.1375283299
Refinement TLS params.Method: refined / Origin x: 14.2084 Å / Origin y: -14.661 Å / Origin z: 16.1114 Å
111213212223313233
T0.147 Å20.0276 Å20.0048 Å2-0.159 Å2-0.0062 Å2--0.1812 Å2
L0.5072 °20.1128 °20.4377 °2-1.1389 °20.0353 °2--1.9362 °2
S-0.0524 Å °-0.0531 Å °0.0075 Å °0.2201 Å °0.0108 Å °-0.0891 Å °0.0244 Å °0.0371 Å °0.0416 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 344
2X-RAY DIFFRACTION1allS1 - 300
3X-RAY DIFFRACTION1allS301
4X-RAY DIFFRACTION1allB402

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