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- PDB-7e4m: Class I Pimarane-Type Diterpene Synthases Stt4548 -

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Basic information

Entry
Database: PDB / ID: 7e4m
TitleClass I Pimarane-Type Diterpene Synthases Stt4548
ComponentsStt4548
KeywordsBIOSYNTHETIC PROTEIN / class I diterpene synthases / pimarane-type diterpenoids
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsYu, J.H. / Xing, B.Y. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877002, 81673332, 81991525, 81573326 China
CitationJournal: Commun Chem / Year: 2021
Title: Functional characterization and structural bases of two class I diterpene synthases in pimarane-type diterpene biosynthesis
Authors: Xing, B. / Yu, J. / Chi, C. / Ma, X. / Xu, Q. / Li, A. / Ge, Y. / Wang, Z. / Liu, T. / Jia, H. / Yin, F. / Guo, J. / Huang, L. / Yang, D. / Ma, M.
History
DepositionFeb 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stt4548


Theoretical massNumber of molelcules
Total (without water)33,7851
Polymers33,7851
Non-polymers00
Water2,144119
1
A: Stt4548

A: Stt4548


Theoretical massNumber of molelcules
Total (without water)67,5712
Polymers67,5712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2920 Å2
ΔGint-25 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.870, 64.908, 70.583
Angle α, β, γ (deg.)90.000, 108.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Stt4548


Mass: 33785.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium chloride, 0.1M BIS-TRIS pH 6.5, 1.5M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.57→66.84 Å / Num. obs: 31104 / % possible obs: 90 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.4
Reflection shellResolution: 1.58→1.68 Å / Num. unique obs: 1555 / Rpim(I) all: 0.468

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→66.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.384 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1583 5.1 %RANDOM
Rwork0.1788 ---
obs0.1804 29525 77.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.35 Å2 / Biso mean: 35.57 Å2 / Biso min: 18.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.01 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.57→66.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 0 119 2158
Biso mean---42.41 -
Num. residues----270
LS refinement shellResolution: 1.57→1.608 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.103 3 -
Rwork0.304 117 -
obs--4 %

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