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- PDB-5guc: Crystal structure of CotB2 (apo form) from Streptomyces melanospo... -

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Basic information

Entry
Database: PDB / ID: 5guc
TitleCrystal structure of CotB2 (apo form) from Streptomyces melanosporofaciens
ComponentsCyclooctat-9-en-7-ol synthase
KeywordsBIOSYNTHETIC PROTEIN / TERPENE CYCLASE FOLD / DITERPENE CYCLASE / LYASE
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
FORMIC ACID / Cyclooctat-9-en-7-ol synthase
Similarity search - Component
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsTomita, T. / Kim, S.-Y. / Ozaki, T. / Yoshida, A. / Kuzuyama, T. / Nishiyama, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS26292058 Japan
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structural Insights into the CotB2-Catalyzed Cyclization of Geranylgeranyl Diphosphate to the Diterpene Cyclooctat-9-en-7-ol
Authors: Tomita, T. / Kim, S.-Y. / Teramoto, K. / Meguro, A. / Ozaki, T. / Yoshida, A. / Motoyoshi, Y. / Mori, N. / Ishigami, K. / Watanabe, H. / Nishiyama, M. / Kuzuyama, T.
History
DepositionAug 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)76,4764
Polymers76,3842
Non-polymers922
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-20 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.274, 101.182, 106.991
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 / Geranylgeranyl Diphosphate Cyclase


Mass: 38192.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria)
Gene: CotB2 / Plasmid: PHIS8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M HEPES-NAOH (PH8.0), 1.4M AMMONIUM FORMATE

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 22, 2009
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.32 Å / Num. obs: 62332 / % possible obs: 99.5 % / Observed criterion σ(I): 2.9 / Redundancy: 7.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 29
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.515 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
REFMAC5.5.0110refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.812 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3145 5.1 %RANDOM
Rwork0.177 ---
obs0.178 58862 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 30.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 6 419 5015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224752
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9396450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9965570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06423.065248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87615796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2731544
X-RAY DIFFRACTIONr_chiral_restr0.1150.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213680
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6051.52834
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14924612
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94531918
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3084.51832
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 243 -
Rwork0.233 4209 -
obs--98.06 %
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)
13.60720.00680.59452.0286-0.54953.96120.001-0.0611-0.11920.01490.0480.00260.293-0.0847-0.0490.1909-0.01020.00750.09680.0270.1011-21.2154-1.2523-6.473
21.9109-0.2081-0.03432.1303-0.09412.17180.0709-0.14240.04860.10410.01220.2729-0.1746-0.1958-0.08310.1056-0.00010.03220.0868-0.03780.1219-22.117228.0237-8.9376
30.65060.1217-0.08990.9853-0.1361.31330.0227-0.0513-0.02520.04340.01580.08830.0871-0.1049-0.03850.0685-0.0027-0.00050.08710.00430.0827-19.105710.613-16.9711
40.51550.3646-0.17652.32640.37651.06390.0190.11140.028-0.15170.0365-0.0527-0.01110.0961-0.05550.119400.01320.1657-0.01080.0899-6.484612.671-49.1103
50.3685-0.01850.00161.1363-0.20821.37980.01810.00830.0558-0.0606-0.0045-0.1632-0.13950.1794-0.01360.0824-0.02240.01970.1045-0.00530.1132-6.143422.4342-37.1351
61.0134-0.2895-0.23161.29940.36361.41720.00780.0606-0.0498-0.07760.0327-0.06480.09860.0414-0.04040.0625-0.0123-0.00970.065-0.00790.0704-12.56687.2882-39.5024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 39
2X-RAY DIFFRACTION2A40 - 143
3X-RAY DIFFRACTION3A144 - 292
4X-RAY DIFFRACTION4B12 - 72
5X-RAY DIFFRACTION5B73 - 194
6X-RAY DIFFRACTION6B195 - 292

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