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- PDB-7e4n: Crystal structure of Sat1646 -

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Basic information

Entry
Database: PDB / ID: 7e4n
TitleCrystal structure of Sat1646
ComponentsSat1646
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 speciesSalinispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 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 1.1Mar 23, 2022Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Apr 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sat1646
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4194
Polymers33,3461
Non-polymers733
Water2,504139
1
A: Sat1646
hetero molecules

A: Sat1646
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8388
Polymers66,6922
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area4020 Å2
ΔGint-72 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.017, 89.017, 68.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

21A-521-

HOH

31A-530-

HOH

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Components

#1: Protein Sat1646


Mass: 33346.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinispora (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 15% v/v Tacsimate TM pH 7.0, 0.1M HEPES pH 7.0, 2% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 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: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.94→62.95 Å / Num. obs: 18106 / % possible obs: 87 % / Redundancy: 21.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 18
Reflection shellResolution: 1.94→1.99 Å / Rmerge(I) obs: 1.625 / Num. unique obs: 905

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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: 1.94→28.61 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 936 5.17 %
Rwork0.1953 17163 -
obs0.1979 18099 86.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.14 Å2 / Biso mean: 39.0958 Å2 / Biso min: 16.95 Å2
Refinement stepCycle: final / Resolution: 1.94→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 3 139 2409
Biso mean--57.84 40.31 -
Num. residues----290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-2.040.31551110.24722068217974
2.04-2.170.29271070.22761969207671
2.17-2.340.28481500.21592405255587
2.34-2.570.2881560.212427892945100
2.57-2.950.3001930.21762046213972
2.95-3.710.25251580.205328643022100
3.71-28.610.20871610.170130223183100

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