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- PDB-4omg: Crystal structure of the bacterial diterpene cyclase COTB2 -

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Basic information

Entry
Database: PDB / ID: 4omg
TitleCrystal structure of the bacterial diterpene cyclase COTB2
ComponentsGeranylgeranyl diphosphate cyclase
KeywordsLYASE / terpene cyclase / geranylgeranyl diphophate / class I terpene cyclase fold
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 / SAD / Resolution: 1.64 Å
AuthorsJanke, R. / Goerner, C. / Hirte, M. / Brueck, T. / Loll, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The first structure of a bacterial diterpene cyclase: CotB2.
Authors: Janke, R. / Gorner, C. / Hirte, M. / Bruck, T. / Loll, B.
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jan 7, 2015Group: Structure summary
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geranylgeranyl diphosphate cyclase
B: Geranylgeranyl diphosphate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0306
Polymers73,5412
Non-polymers4894
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-46 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.060, 100.650, 108.730
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 Geranylgeranyl diphosphate cyclase


Mass: 36770.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria)
Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 / References: UniProt: C9K1X5
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 20% (v/v)PEG8000, 100 mM 3-(cyclohexylamino)-1-propanesulfonic acid (CAPS), pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2013
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 79406 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.69 Å2 / Net I/σ(I): 17.5

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.64→47.833 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 3902 4.91 %RANDOM
Rwork0.1734 ---
obs0.1747 79406 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→47.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4575 0 30 268 4873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134940
X-RAY DIFFRACTIONf_angle_d1.4246735
X-RAY DIFFRACTIONf_dihedral_angle_d15.0031872
X-RAY DIFFRACTIONf_chiral_restr0.1728
X-RAY DIFFRACTIONf_plane_restr0.007870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.31491380.27612632X-RAY DIFFRACTION99
1.66-1.6810.29071390.25612646X-RAY DIFFRACTION99
1.681-1.70310.27931400.24322663X-RAY DIFFRACTION99
1.7031-1.72650.27051400.22952654X-RAY DIFFRACTION99
1.7265-1.75110.23591410.22582675X-RAY DIFFRACTION99
1.7511-1.77730.26571390.22482648X-RAY DIFFRACTION99
1.7773-1.80510.22781420.21882697X-RAY DIFFRACTION99
1.8051-1.83470.25251390.20612626X-RAY DIFFRACTION99
1.8347-1.86630.2008770.19762732X-RAY DIFFRACTION99
1.8663-1.90020.25811470.18562688X-RAY DIFFRACTION99
1.9002-1.93680.20821380.18342653X-RAY DIFFRACTION99
1.9368-1.97630.21491470.17212670X-RAY DIFFRACTION99
1.9763-2.01930.20991350.1752674X-RAY DIFFRACTION99
2.0193-2.06630.2161390.17282658X-RAY DIFFRACTION99
2.0663-2.11790.24191350.172695X-RAY DIFFRACTION99
2.1179-2.17520.17781490.16682675X-RAY DIFFRACTION99
2.1752-2.23920.20681350.16422690X-RAY DIFFRACTION99
2.2392-2.31150.22241460.16422685X-RAY DIFFRACTION99
2.3115-2.39410.18651380.16082696X-RAY DIFFRACTION99
2.3941-2.48990.17551440.15492683X-RAY DIFFRACTION99
2.4899-2.60320.19161450.1652699X-RAY DIFFRACTION99
2.6032-2.74050.181360.16972725X-RAY DIFFRACTION100
2.7405-2.91220.21721450.16882725X-RAY DIFFRACTION100
2.9122-3.1370.19871450.17582737X-RAY DIFFRACTION100
3.137-3.45260.21121470.16692740X-RAY DIFFRACTION99
3.4526-3.9520.17241430.15862754X-RAY DIFFRACTION99
3.952-4.97820.15261470.1512798X-RAY DIFFRACTION99
4.9782-47.85360.19571460.18422886X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8464-0.03530.17891.34-0.12391.62290.017-0.0534-0.00880.13220.01820.108-0.1193-0.1463-0.02480.1191-0.00360.01240.12190.0070.0933-20.757714.9891-12.9523
20.87530.07160.13381.3419-0.08961.64490.0250.0839-0.0054-0.04860.0164-0.1133-0.09280.1356-0.0370.1123-0.02470.00310.129-0.00760.0879-9.872915.3506-41.0717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 16:295)
2X-RAY DIFFRACTION2(chain B and resid 14:292)

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