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- PDB-4omh: Crystal structure of the bacterial diterpene cyclase COTB2 varian... -

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Basic information

Entry
Database: PDB / ID: 4omh
TitleCrystal structure of the bacterial diterpene cyclase COTB2 variant F149L
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 / MOLECULAR REPLACEMENT / 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: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_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)73,9626
Polymers73,4732
Non-polymers4894
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-39 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.480, 98.360, 107.830
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: 36736.508 Da / Num. of mol.: 2 / Mutation: F149L
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.: 303 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 15% (v/v) PEG8000, 60 mM 3-(cyclohexylamino)-1-propanesulfonic acid (CAPS), 2% (v/v) 2-methyl-2,4-pentanediol (MPD), 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: 77073 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 19.14 Å2 / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→47.278 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 3760 4.88 %RANDOM
Rwork0.1833 ---
obs0.1849 77073 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→47.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 30 303 4921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124991
X-RAY DIFFRACTIONf_angle_d1.4376815
X-RAY DIFFRACTIONf_dihedral_angle_d15.141908
X-RAY DIFFRACTIONf_chiral_restr0.097742
X-RAY DIFFRACTIONf_plane_restr0.008883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.66080.29711390.24342637X-RAY DIFFRACTION97
1.6608-1.68270.23441390.22452636X-RAY DIFFRACTION98
1.6827-1.70570.24451390.20512639X-RAY DIFFRACTION98
1.7057-1.73010.23771400.1912663X-RAY DIFFRACTION98
1.7301-1.75590.22411410.19052680X-RAY DIFFRACTION98
1.7559-1.78330.2551700.19222722X-RAY DIFFRACTION98
1.7833-1.81260.25011340.18282683X-RAY DIFFRACTION98
1.8126-1.84380.25041350.17562661X-RAY DIFFRACTION98
1.8438-1.87740.19631310.16952695X-RAY DIFFRACTION98
1.8774-1.91350.19351470.17882685X-RAY DIFFRACTION99
1.9135-1.95250.22641370.17662694X-RAY DIFFRACTION98
1.9525-1.9950.20731420.17052671X-RAY DIFFRACTION98
1.995-2.04140.21241400.16822692X-RAY DIFFRACTION99
2.0414-2.09240.2081480.16512720X-RAY DIFFRACTION99
2.0924-2.1490.21751370.16312682X-RAY DIFFRACTION99
2.149-2.21230.20381470.16162710X-RAY DIFFRACTION99
2.2123-2.28370.18071390.1572732X-RAY DIFFRACTION99
2.2837-2.36530.2021410.15942700X-RAY DIFFRACTION99
2.3653-2.460.19521440.16472707X-RAY DIFFRACTION99
2.46-2.57190.20731450.16882725X-RAY DIFFRACTION99
2.5719-2.70750.1951360.17182750X-RAY DIFFRACTION100
2.7075-2.87710.22621540.1752734X-RAY DIFFRACTION100
2.8771-3.09920.23171400.18312764X-RAY DIFFRACTION99
3.0992-3.4110.20531480.18542781X-RAY DIFFRACTION100
3.411-3.90440.20281450.18392780X-RAY DIFFRACTION99
3.9044-4.91830.21351490.18942840X-RAY DIFFRACTION100
4.9183-47.29790.2411530.2242930X-RAY DIFFRACTION99
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)
10.72680.0183-0.13411.68250.06021.20640.02650.04070.0325-0.06560.0267-0.13630.02450.1242-0.04630.09510.00260.00440.1279-0.00840.085918.1107-82.6976120.816
20.8408-0.10360.0291.8489-0.12661.23270.0431-0.05640.0180.1742-0.00290.1909-0.0267-0.0931-0.02940.1245-0.00130.01860.1130.00780.10276.7306-84.2064148.6947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 13:292)
2X-RAY DIFFRACTION2(chain B and resid 13:294)

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