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- PDB-6m7f: Wild-type Cucumene Synthase -

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Basic information

Entry
Database: PDB / ID: 6m7f
TitleWild-type Cucumene Synthase
ComponentsCucumene Synthase
KeywordsLYASE / Triquinane Scaffold / Open Conformation / Terpene Cyclase
Function / homologyLyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / Terpene synthase / Terpene synthase
Function and homology information
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.051 Å
AuthorsBlank, P.N. / Pemberton, T.A. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)GM56838 United States
CitationJournal: Biochemistry / Year: 2018
Title: Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene.
Authors: Blank, P.N. / Pemberton, T.A. / Chow, J.Y. / Poulter, C.D. / Christianson, D.W.
History
DepositionAug 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cucumene Synthase
B: Cucumene Synthase
C: Cucumene Synthase
D: Cucumene Synthase


Theoretical massNumber of molelcules
Total (without water)155,0504
Polymers155,0504
Non-polymers00
Water724
1
A: Cucumene Synthase
B: Cucumene Synthase


Theoretical massNumber of molelcules
Total (without water)77,5252
Polymers77,5252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-29 kcal/mol
Surface area21610 Å2
MethodPISA
2
C: Cucumene Synthase
D: Cucumene Synthase


Theoretical massNumber of molelcules
Total (without water)77,5252
Polymers77,5252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-27 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.741, 95.846, 102.299
Angle α, β, γ (deg.)90.00, 96.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cucumene Synthase


Mass: 38762.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (strain ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602) (bacteria)
Strain: ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602
Gene: SSCG_00251 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B5GLM7, UniProt: D5SLU6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG 3350, 0.1mM Bis-Tris

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→29.9 Å / Num. obs: 23205 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.093 / Net I/σ(I): 5.7
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.672 / Num. unique obs: 23205 / CC1/2: 0.876 / Rpim(I) all: 0.424 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1


Resolution: 3.051→29.897 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.19
RfactorNum. reflection% reflection
Rfree0.2993 1153 5 %
Rwork0.2444 --
obs0.2472 23077 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.051→29.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7825 0 0 4 7829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038057
X-RAY DIFFRACTIONf_angle_d0.57311002
X-RAY DIFFRACTIONf_dihedral_angle_d14.2084676
X-RAY DIFFRACTIONf_chiral_restr0.0371227
X-RAY DIFFRACTIONf_plane_restr0.0061428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0511-3.18990.4091360.34272633X-RAY DIFFRACTION94
3.1899-3.35780.33831440.30542704X-RAY DIFFRACTION99
3.3578-3.56790.34871330.28962752X-RAY DIFFRACTION99
3.5679-3.84280.32121570.23972732X-RAY DIFFRACTION100
3.8428-4.22860.25081530.2222750X-RAY DIFFRACTION99
4.2286-4.83820.28211440.21552780X-RAY DIFFRACTION100
4.8382-6.08720.29891470.24462769X-RAY DIFFRACTION100
6.0872-29.8980.2671390.21532804X-RAY DIFFRACTION98

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