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- PDB-7y87: class I diterpene synthase mutant (CyS-C59A) from Streptomyces ca... -

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Basic information

Entry
Database: PDB / ID: 7y87
Titleclass I diterpene synthase mutant (CyS-C59A) from Streptomyces cattleya
ComponentsPutative glutamate dehydrogenase/leucine dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / class I diterpene synthase mutant (CyS-C59A) from Streptomyces cattleya
Function / homologycattleyene synthase / Terpene cyclase-like 2 / terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / metal ion binding / Cattleyene synthase
Function and homology information
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXing, B. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877002, 22077007 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes.
Authors: Xing, B. / Xu, H. / Li, A. / Lou, T. / Xu, M. / Wang, K. / Xu, Z. / Dickschat, J.S. / Yang, D. / Ma, M.
History
DepositionJun 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 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: Putative glutamate dehydrogenase/leucine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)42,0181
Polymers42,0181
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.284, 112.628, 137.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-526-

HOH

31A-626-

HOH

41A-666-

HOH

51A-669-

HOH

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Components

#1: Protein Putative glutamate dehydrogenase/leucine dehydrogenase / CyS


Mass: 42018.492 Da / Num. of mol.: 1 / Mutation: C59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (bacteria)
Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057
Gene: SCATT_p16530 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8JK18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.49 M Sodium phosphate monobasic monohydrate, 0.91 M Potassium phosphate dibasic, pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.3→29.3 Å / Num. obs: 98052 / % possible obs: 99.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.26 / Num. unique obs: 17379

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7y50

7y50


Resolution: 2.3→29.3 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 1738 10.01 %
Rwork0.1877 15632 -
obs0.1924 17370 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.47 Å2 / Biso mean: 19.473 Å2 / Biso min: 2.57 Å2
Refinement stepCycle: final / Resolution: 2.3→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 0 289 3049
Biso mean---22.22 -
Num. residues----352
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.370.30511410.2415127399
2.37-2.440.26851440.18051294100
2.44-2.530.251440.19991295100
2.53-2.630.25131440.19941290100
2.63-2.750.26721430.18731294100
2.75-2.90.25171440.19541297100
2.9-3.080.23951440.20671289100
3.08-3.320.24941450.20671306100
3.32-3.650.2481440.1949129699
3.65-4.180.2051440.1755129798
4.18-5.260.18181470.14491322100
5.26-29.30.20621540.1791137999

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