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- PDB-6ggk: Crystal structure of CotB2 C-terminal truncation -

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Basic information

Entry
Database: PDB / ID: 6ggk
TitleCrystal structure of CotB2 C-terminal truncation
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
Cyclooctat-9-en-7-ol synthase
Similarity search - Component
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: Cyclooctat-9-en-7-ol synthase
B: Cyclooctat-9-en-7-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7836
Polymers67,6752
Non-polymers1084
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-53 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.010, 99.714, 107.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33837.309 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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 16% (v/v) polyethylene glycol 4000, 100 mM Tris at pH 8.5, 100 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 36510 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rrim(I) all: 0.333 / Net I/σ(I): 6.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5766 / Rrim(I) all: 2.087 / % possible all: 99

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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: 2.15→49.857 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.241 1825 5 %
Rwork0.1982 --
obs0.2004 36480 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→49.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4537 0 4 197 4738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074659
X-RAY DIFFRACTIONf_angle_d0.8066324
X-RAY DIFFRACTIONf_dihedral_angle_d2.3983313
X-RAY DIFFRACTIONf_chiral_restr0.046691
X-RAY DIFFRACTIONf_plane_restr0.005817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1479-2.2060.34331350.30032580X-RAY DIFFRACTION98
2.206-2.27090.34291380.28642616X-RAY DIFFRACTION100
2.2709-2.34420.28941400.26052642X-RAY DIFFRACTION100
2.3442-2.4280.27921380.24622625X-RAY DIFFRACTION100
2.428-2.52520.31951390.24182647X-RAY DIFFRACTION100
2.5252-2.64010.2571400.23292645X-RAY DIFFRACTION100
2.6401-2.77930.29541390.22222647X-RAY DIFFRACTION100
2.7793-2.95340.26581380.19912628X-RAY DIFFRACTION100
2.9534-3.18140.25871420.19892692X-RAY DIFFRACTION100
3.1814-3.50150.23311390.17882653X-RAY DIFFRACTION100
3.5015-4.0080.19021430.15742704X-RAY DIFFRACTION100
4.008-5.04890.19011430.15352729X-RAY DIFFRACTION100
5.0489-49.87040.19891510.18172847X-RAY DIFFRACTION100

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