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- PDB-6ggi: Crystal structure of CotB2 in complex with 2-fluoro-3,7,18-dolabe... -

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Basic information

Entry
Database: PDB / ID: 6ggi
TitleCrystal structure of CotB2 in complex with 2-fluoro-3,7,18-dolabellatriene
ComponentsCyclooctat-9-en-7-ol synthase
KeywordsLYASE / terpene synthase / cyclooctatin
Function / homology
Function and homology information


cyclooctat-9-en-7-ol synthase / isomerase activity / lyase activity / metal ion binding
Similarity search - Function
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
ACETONITRILE / 2-fluoro-3,7,18-dolabellatriene / : / DI(HYDROXYETHYL)ETHER / PYROPHOSPHATE / Cyclooctat-9-en-7-ol synthase
Similarity search - Component
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsDriller, R. / Janke, S. / Fuchs, M. / Warner, E. / Mhashal, A.R. / Major, D.T. / Christmann, M. / Brueck, T. / Loll, B.
CitationJournal: Nat Commun / Year: 2018
Title: Towards a comprehensive understanding of the structural dynamics of a bacterial diterpene synthase during catalysis.
Authors: Driller, R. / Janke, S. / Fuchs, M. / Warner, E. / Mhashal, A.R. / Major, D.T. / Christmann, M. / Bruck, T. / Loll, B.
History
DepositionMay 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclooctat-9-en-7-ol synthase
B: Cyclooctat-9-en-7-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,37125
Polymers73,5412
Non-polymers1,83023
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-146 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.885, 98.722, 105.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cyclooctat-9-en-7-ol synthase


Mass: 36770.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria)
Gene: CotB2 / Production host: Escherichia coli (E. coli) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase

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Non-polymers , 9 types, 306 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical ChemComp-EXW / 2-fluoro-3,7,18-dolabellatriene


Mass: 290.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H31F
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 30% (v/v) polyethylene glycol 400, 100 mM HEPES at pH 7.5 and 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2015
RadiationMonochromator: SI111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→44.74 Å / Num. obs: 61262 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rrim(I) all: 0.114 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.87 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 9672 / Rrim(I) all: 1.146 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OMG

4omg


Resolution: 1.803→44.737 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.03
RfactorNum. reflection% reflection
Rfree0.1995 2097 3.43 %
Rwork0.1695 --
obs0.1706 61142 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.803→44.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4847 0 107 283 5237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125141
X-RAY DIFFRACTIONf_angle_d1.2916993
X-RAY DIFFRACTIONf_dihedral_angle_d6.384203
X-RAY DIFFRACTIONf_chiral_restr0.088764
X-RAY DIFFRACTIONf_plane_restr0.007895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8029-1.84490.2781340.26893769X-RAY DIFFRACTION97
1.8449-1.8910.32711380.25013903X-RAY DIFFRACTION99
1.891-1.94210.25641360.22543853X-RAY DIFFRACTION99
1.9421-1.99930.26591390.21013914X-RAY DIFFRACTION100
1.9993-2.06380.26711380.19313880X-RAY DIFFRACTION99
2.0638-2.13760.22461390.18183905X-RAY DIFFRACTION100
2.1376-2.22320.21061400.16563918X-RAY DIFFRACTION100
2.2232-2.32430.19641400.1573951X-RAY DIFFRACTION100
2.3243-2.44690.19831390.15183897X-RAY DIFFRACTION100
2.4469-2.60020.19491400.15433962X-RAY DIFFRACTION100
2.6002-2.80090.18971400.15163939X-RAY DIFFRACTION100
2.8009-3.08270.16181410.15243976X-RAY DIFFRACTION100
3.0827-3.52860.17211420.15093991X-RAY DIFFRACTION100
3.5286-4.44510.1651430.14534014X-RAY DIFFRACTION100
4.4451-44.75050.20391480.18874173X-RAY DIFFRACTION99

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