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- PDB-7e4o: Class I Pimarane-Type Diterpene Synthases from Actinomycetes -

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Basic information

Entry
Database: PDB / ID: 7e4o
TitleClass I Pimarane-Type Diterpene Synthases from Actinomycetes
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3Nov 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: Sat1646


Theoretical massNumber of molelcules
Total (without water)33,3461
Polymers33,3461
Non-polymers00
Water1,00956
1
A: Sat1646

A: Sat1646


Theoretical massNumber of molelcules
Total (without water)66,6922
Polymers66,6922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.013, 89.013, 70.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
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: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 10288 / % possible obs: 100 % / Redundancy: 25.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 45
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 25.9 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1001

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E4N

7e4n


Resolution: 2.5→27.36 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 1016 10.01 %
Rwork0.2228 9129 -
obs0.228 10145 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.72 Å2 / Biso mean: 71.4443 Å2 / Biso min: 43.82 Å2
Refinement stepCycle: final / Resolution: 2.5→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 0 56 2307
Biso mean---64.13 -
Num. residues----289
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 (%)
2.5-2.630.36971380.28651249138797
2.64-2.80.33011420.27341258140098
2.8-3.020.33861420.27711276141899
3.02-3.320.32331450.268513021447100
3.32-3.80.33631450.224513111456100
3.8-4.780.25071480.206213281476100
4.78-27.360.22021560.19321405156199
Refinement TLS params.Method: refined / Origin x: -14.7481 Å / Origin y: -34.1284 Å / Origin z: -8.3305 Å
111213212223313233
T0.5823 Å20.0465 Å20.0639 Å2-0.4825 Å20.006 Å2--0.523 Å2
L1.6928 °2-0.7568 °20.0339 °2-0.6516 °2-0.0367 °2--1.1777 °2
S0.1604 Å °0.1601 Å °0.072 Å °-0.2568 Å °-0.1711 Å °-0.3317 Å °-0.0682 Å °-0.134 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 291
2X-RAY DIFFRACTION1allS1 - 67

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