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- PDB-6ggj: Crystal structure of CotB2 in complex with alendronate -

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Basic information

Entry
Database: PDB / ID: 6ggj
TitleCrystal structure of CotB2 in complex with alendronate
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
4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / Cyclooctat-9-en-7-ol synthase
Similarity search - Component
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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

Downloads & links

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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)74,17710
Polymers73,5412
Non-polymers6368
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-73 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.380, 56.460, 56.930
Angle α, β, γ (deg.)91.82, 101.66, 115.93
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical ChemComp-AHD / 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / ALENDRONATE / FOSAMAX (TM)


Mass: 245.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 26% (v/v) polyethylene glycol 4000, 100 mM Tris at pH 8.5, 150 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: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2017
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 33594 / % possible obs: 99.1 % / Redundancy: 3.1 % / Rrim(I) all: 0.14 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2485 / Rrim(I) all: 0.92 / % possible all: 99.1

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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: 2.1→19.83 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.29
RfactorNum. reflection% reflection
Rfree0.2367 1680 5 %
Rwork0.1828 --
obs0.1856 33590 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4734 0 34 223 4991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074904
X-RAY DIFFRACTIONf_angle_d0.8456663
X-RAY DIFFRACTIONf_dihedral_angle_d4.7854054
X-RAY DIFFRACTIONf_chiral_restr0.046723
X-RAY DIFFRACTIONf_plane_restr0.006856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16170.33191400.26482665X-RAY DIFFRACTION99
2.1617-2.23140.31561390.24462647X-RAY DIFFRACTION99
2.2314-2.3110.311410.2412660X-RAY DIFFRACTION99
2.311-2.40340.2991400.21582660X-RAY DIFFRACTION99
2.4034-2.51260.33351400.21052660X-RAY DIFFRACTION100
2.5126-2.64480.23921390.20432654X-RAY DIFFRACTION100
2.6448-2.810.2971420.20382684X-RAY DIFFRACTION99
2.81-3.02630.26081380.19342638X-RAY DIFFRACTION99
3.0263-3.32960.25761420.18952688X-RAY DIFFRACTION100
3.3296-3.80840.2191390.16322640X-RAY DIFFRACTION99
3.8084-4.7870.17751400.14252669X-RAY DIFFRACTION100
4.787-19.83090.16891400.15132645X-RAY DIFFRACTION99

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