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- PDB-5gue: Crystal structure of CotB2 (GGSPP/Mg2+-Bound Form) from Streptomy... -

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Basic information

Entry
Database: PDB / ID: 5gue
TitleCrystal structure of CotB2 (GGSPP/Mg2+-Bound 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
Chem-GGS / Cyclooctat-9-en-7-ol synthase
Similarity search - Component
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Nov 8, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Cyclooctat-9-en-7-ol synthase
D: Cyclooctat-9-en-7-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,73212
Polymers152,7694
Non-polymers1,9638
Water15,241846
1
A: Cyclooctat-9-en-7-ol synthase
B: Cyclooctat-9-en-7-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3666
Polymers76,3842
Non-polymers9824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-22 kcal/mol
Surface area22100 Å2
MethodPISA
2
C: Cyclooctat-9-en-7-ol synthase
D: Cyclooctat-9-en-7-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3666
Polymers76,3842
Non-polymers9824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-21 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.698, 100.373, 108.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cyclooctat-9-en-7-ol synthase / Geranylgeranyl Diphosphate Cyclase


Mass: 38192.129 Da / Num. of mol.: 4
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-GGS / phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid


Mass: 466.509 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H36O6P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M BICINE-NAOH (PH9.0), 20% PEG 6000

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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: Oct 23, 2009
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→34.15 Å / Num. obs: 116825 / % possible obs: 99.1 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 17.9
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.641 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.5.0110refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5GUC

5guc


Resolution: 1.8→34.15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.632 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5798 5 %RANDOM
Rwork0.191 ---
obs0.193 109934 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.07 Å2
2---0.13 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9344 0 120 846 10310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.95213154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18451140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73623.092498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.843151618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8471586
X-RAY DIFFRACTIONr_chiral_restr0.1160.21418
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217486
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_it0.7641.55710
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41829292
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23133996
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6314.53860
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
Rfree0.339 436 -
Rwork0.291 8060 -
obs--98.7 %
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)
10.1304-0.02550.06640.19090.04980.89730.01930.01720.0123-0.01250.01460.00010.0126-0.062-0.0340.007-0.00330.00410.01940.00840.05349.7752-15.0052-14.2409
20.01210.00630.04850.27030.12451.02130.0061-0.00620.01750.03350.0471-0.00390.03990.0521-0.05320.01470.00050.00120.0207-0.01490.051220.2047-14.760414.4276
30.1216-0.0466-0.05090.1709-0.0330.93310.0190.0158-0.0042-0.01250.0233-0.0009-0.00240.0644-0.04240.0073-0.00230.00780.0224-0.00810.053919.542615.734740.2584
40.02280.0196-0.04620.2216-0.11491.07280.0091-0.01-0.02290.02590.04030.0021-0.0389-0.0539-0.04940.0138-0.00140.0070.02110.01470.05289.077115.443468.8213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 296
2X-RAY DIFFRACTION2B12 - 296
3X-RAY DIFFRACTION3C12 - 296
4X-RAY DIFFRACTION4D12 - 296

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