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- PDB-5dw7: Crystal structure of the unliganded geosmin synthase N-terminal d... -

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Basic information

Entry
Database: PDB / ID: 5dw7
TitleCrystal structure of the unliganded geosmin synthase N-terminal domain from Streptomyces coelicolor
ComponentsGermacradienol/geosmin synthase
KeywordsLYASE / terpene cyclase
Function / homology
Function and homology information


geosmin synthase / germacradienol synthase / (-)-germacrene D synthase / germacradienol synthase activity / germacrene-D synthase activity / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Germacradienol/geosmin synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.202 Å
AuthorsLombardi, P.M. / Harris, G.G. / Pemberton, T.A. / Matsui, T. / Weiss, T.M. / Cole, K.E. / Koksal, M. / Murphy, F.V. / Vedula, L.S. / Chou, W.K. ...Lombardi, P.M. / Harris, G.G. / Pemberton, T.A. / Matsui, T. / Weiss, T.M. / Cole, K.E. / Koksal, M. / Murphy, F.V. / Vedula, L.S. / Chou, W.K. / Cane, D.E. / Christianson, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM30301 United States
CitationJournal: Biochemistry / Year: 2015
Title: Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with alpha alpha Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence.
Authors: Harris, G.G. / Lombardi, P.M. / Pemberton, T.A. / Matsui, T. / Weiss, T.M. / Cole, K.E. / Koksal, M. / Murphy, F.V. / Vedula, L.S. / Chou, W.K. / Cane, D.E. / Christianson, D.W.
History
DepositionSep 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Germacradienol/geosmin synthase


Theoretical massNumber of molelcules
Total (without water)40,9551
Polymers40,9551
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.780, 76.780, 130.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Germacradienol/geosmin synthase / ScGS


Mass: 40954.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: cyc2, SCO6073, SC9B1.20 / Plasmid: pET-21d / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X839, germacradienol synthase, (-)-germacrene D synthase, geosmin synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1 M Tris, pH 8.2, 0.5 M magnesium chloride, 28% PEG400
PH range: 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2008
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.202→34.34 Å / Num. all: 6883 / Num. obs: 6127 / % possible obs: 89.13 % / Redundancy: 3.7 % / Biso Wilson estimate: 54.18 Å2 / Rmerge(I) obs: 0.201 / Net I/σ(I): 6.99
Reflection shellResolution: 3.202→3.316 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4 / % possible all: 78.52

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PS1

1ps1


Resolution: 3.202→34.337 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 534 4.88 %
Rwork0.2405 --
obs0.2428 6088 89.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.202→34.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 0 6 2359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022427
X-RAY DIFFRACTIONf_angle_d0.673323
X-RAY DIFFRACTIONf_dihedral_angle_d9.673814
X-RAY DIFFRACTIONf_chiral_restr0.025363
X-RAY DIFFRACTIONf_plane_restr0.004429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2021-3.52410.36651190.2792324X-RAY DIFFRACTION80
3.5241-4.03340.34661230.26562540X-RAY DIFFRACTION87
4.0334-5.0790.25311510.22122706X-RAY DIFFRACTION93
5.079-34.3390.24551410.22522834X-RAY DIFFRACTION97

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