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- PDB-7y88: class I diterpene synthase (CyS-GGPP-Mg2+) from Streptomyces cattleya -

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Basic information

Entry
Database: PDB / ID: 7y88
Titleclass I diterpene synthase (CyS-GGPP-Mg2+) from Streptomyces cattleya
ComponentsPutative glutamate dehydrogenase/leucine dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / class I diterpene synthase (CyS-GGPP-Mg2+) / Streptomyces cattleya
Function / homologycattleyene synthase / : / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / GERANYLGERANYL DIPHOSPHATE / Cattleyene synthase
Function and homology information
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5504
Polymers42,0511
Non-polymers4993
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-23 kcal/mol
Surface area15280 Å2
Unit cell
Length a, b, c (Å)100.560, 113.137, 138.052
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-565-

HOH

21A-649-

HOH

31A-806-

HOH

41A-817-

HOH

51A-818-

HOH

61A-827-

HOH

71A-830-

HOH

81A-836-

HOH

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Components

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


Mass: 42050.559 Da / Num. of mol.: 1
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: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1000 mM Sodium citrate tribasic and 100 mM Sodium cacodylate / Hydrochloric acid pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.87→56.57 Å / Num. obs: 32571 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shellResolution: 1.87→1.91 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 3231

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y50

7y50


Resolution: 1.87→43.753 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 1996 6.13 %
Rwork0.1812 30575 -
obs0.1827 32571 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.6 Å2 / Biso mean: 25.2424 Å2 / Biso min: 9.37 Å2
Refinement stepCycle: final / Resolution: 1.87→43.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 31 336 3141
Biso mean--29.45 30.63 -
Num. residues----354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.87-1.920.26251410.209121632304
1.92-1.970.23651410.212421602301
1.97-2.030.24021400.193821682308
2.03-2.090.22561420.18721562298
2.09-2.170.23271400.187821442284
2.17-2.250.1941420.191821712313
2.25-2.360.24521410.185621792320
2.36-2.480.22671410.189221602301
2.48-2.640.22771430.195621872330
2.64-2.840.21321420.187621772319
2.84-3.120.20551440.195321912335
3.12-3.580.2091440.171522132357
3.58-4.50.15291450.160522132358
4.51-43.750.19551500.168422932443

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