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- PDB-5dz2: Geosmin synthase from Streptomyces coelicolor N-terminal domain c... -

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Basic information

Entry
Database: PDB / ID: 5dz2
TitleGeosmin synthase from Streptomyces coelicolor N-terminal domain complexed with three Mg2+ ions and alendronic acid
ComponentsGermacradienol/geosmin synthase
KeywordsLYASE / terpene / cyclase / geosmin / germacradienol
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
ALENDRONATE / Germacradienol/geosmin synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.111 Å
AuthorsHarris, 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.W. ...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.W. / Cane, D.E. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 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 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Sep 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 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Germacradienol/geosmin synthase
B: Germacradienol/geosmin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,17810
Polymers76,5342
Non-polymers6448
Water2,612145
1
A: Germacradienol/geosmin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5895
Polymers38,2671
Non-polymers3224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Germacradienol/geosmin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5895
Polymers38,2671
Non-polymers3224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.213, 67.213, 345.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-575-

HOH

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Components

#1: Protein Germacradienol/geosmin synthase / ScGS


Mass: 38266.891 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-338)
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: pET22bMV / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X839, germacradienol synthase, (-)-germacrene D synthase, geosmin synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-212 / ALENDRONATE / (4-AMINO-1-HYDROXY-1-PHOSPHONO-BUTYL)PHOSPHONIC ACID / Alendronic acid


Mass: 249.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H13NO7P2 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium acetate trihydrate, pH 7.0, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 46408 / % possible obs: 98.8 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 14.64
Reflection shellResolution: 2.11→2.18 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 1.68 / % possible all: 96.9

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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 5DW7

5dw7


Resolution: 2.111→48.172 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 2275 4.92 %
Rwork0.2074 --
obs0.2096 46193 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.111→48.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 34 145 5232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055285
X-RAY DIFFRACTIONf_angle_d0.9147231
X-RAY DIFFRACTIONf_dihedral_angle_d13.4231907
X-RAY DIFFRACTIONf_chiral_restr0.035768
X-RAY DIFFRACTIONf_plane_restr0.005938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1107-2.15650.36821190.30622607X-RAY DIFFRACTION96
2.1565-2.20670.34061210.28672699X-RAY DIFFRACTION99
2.2067-2.26190.30671490.28012729X-RAY DIFFRACTION99
2.2619-2.3230.38731580.27292704X-RAY DIFFRACTION100
2.323-2.39140.30151320.25652755X-RAY DIFFRACTION100
2.3914-2.46860.2981450.22942708X-RAY DIFFRACTION99
2.4686-2.55680.28681450.21922731X-RAY DIFFRACTION99
2.5568-2.65920.26691180.22182757X-RAY DIFFRACTION99
2.6592-2.78020.29351340.23112768X-RAY DIFFRACTION99
2.7802-2.92680.28381620.2282697X-RAY DIFFRACTION98
2.9268-3.11010.3071510.22972742X-RAY DIFFRACTION99
3.1101-3.35020.2551530.21852743X-RAY DIFFRACTION98
3.3502-3.68720.24381330.20022747X-RAY DIFFRACTION97
3.6872-4.22050.1971310.17192732X-RAY DIFFRACTION95
4.2205-5.31630.18691500.172777X-RAY DIFFRACTION96
5.3163-48.1850.22691740.1913022X-RAY DIFFRACTION98

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