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- PDB-4okm: Selinadiene Synthase apo and in complex with diphosphate -

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Basic information

Entry
Database: PDB / ID: 4okm
TitleSelinadiene Synthase apo and in complex with diphosphate
ComponentsTerpene synthase metal-binding domain-containing protein
KeywordsTRANSFERASE / Sesquiterpene / cyclase / terpenoid / induced fit / open and closed conformation / pyrophosphate sensor
Function / homology
Function and homology information


selina-4(15),7(11)-diene synthase / terpene synthase activity / terpenoid biosynthetic process / magnesium ion binding
Similarity search - Function
: / Terpene cyclase-like 2 / 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
PYROPHOSPHATE / Selina-4(15),7(11)-diene synthase ((2E,6E)-farnesyl diphosphate cyclizing)
Similarity search - Component
Biological speciesStreptomyces pristinaespiralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBaer, P. / Rabe, P. / Fischer, K. / Citron, C.A. / Klapschinski, T. / Groll, M. / Dickschat, J.S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Induced-fit mechanism in class i terpene cyclases.
Authors: Baer, P. / Rabe, P. / Fischer, K. / Citron, C.A. / Klapschinski, T.A. / Groll, M. / Dickschat, J.S.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Feb 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_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_atom_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_auth_seq_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_atom_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terpene synthase metal-binding domain-containing protein
B: Terpene synthase metal-binding domain-containing protein
C: Terpene synthase metal-binding domain-containing protein
D: Terpene synthase metal-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,88616
Polymers165,1344
Non-polymers75312
Water14,124784
1
A: Terpene synthase metal-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5345
Polymers41,2831
Non-polymers2514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terpene synthase metal-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5345
Polymers41,2831
Non-polymers2514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Terpene synthase metal-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5345
Polymers41,2831
Non-polymers2514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Terpene synthase metal-binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)41,2831
Polymers41,2831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.780, 119.090, 186.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.856045, -0.017088, -0.516618), (-0.021251, -0.997445, 0.068205), (-0.516464, 0.069365, 0.853495)-140.70021, 230.04688, -47.70896
3given(-0.775762, 0.380474, 0.503421), (0.386621, 0.917087, -0.097337), (-0.498716, 0.119123, -0.858541)-195.48509, 40.73876, -27.85269

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Components

#1: Protein
Terpene synthase metal-binding domain-containing protein


Mass: 41283.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces pristinaespiralis (bacteria)
Gene: SSDG_02809, ZP_06911744 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5HDJ6, squalene synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M TRIS, 200 mM MgCl2, 24% PEG 3350, 1 mM farnesyl pyrophosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.6 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 97702 / Num. obs: 94771 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.153 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.5 / % possible all: 95.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet model of Selinadiene Synthase (experimental phasing)

Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.186 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20265 4737 5 %RANDOM
Rwork0.15696 ---
obs0.15924 89987 97 %-
all-94724 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0 Å2
2--2.97 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10707 0 36 784 11527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01910996
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210239
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.95314980
X-RAY DIFFRACTIONr_angle_other_deg0.756323441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93351337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00822.904551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.667151739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.03915116
X-RAY DIFFRACTIONr_chiral_restr0.0580.21630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112503
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022643
X-RAY DIFFRACTIONr_rigid_bond_restr1.522321235
X-RAY DIFFRACTIONr_sphericity_free28.8335249
X-RAY DIFFRACTIONr_sphericity_bonded6.188521517
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 333 -
Rwork0.219 6324 -
obs--95.29 %
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)
10.35560.0534-0.00090.10950.02230.30430.00550.01120.00350.01240.0158-0.02280.01230.066-0.02130.00190.0049-0.00210.0231-0.01350.07-72.0246119.978743.0372
20.19090.0418-0.01530.11950.06220.3766-0.00780.01090.0081-0.00060.0098-0.00430.0303-0.0654-0.0020.0212-0.01050.00130.0169-0.00430.0604-103.3329114.948834.4302
30.1395-0.0015-0.06870.08730.0610.58790.0323-0.0003-0.008-0.0001-0.01380.0062-0.0998-0.051-0.01850.05780.01720.00950.00860.0030.0504-100.5213128.0551-6.3903
40.1881-0.0776-0.25440.21330.05250.4109-0.0131-0.06190.0048-0.00070.0163-0.01340.03630.1307-0.00310.02590.0239-0.00670.06080.00330.0531-75.4132110.5917-15.6335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 349
2X-RAY DIFFRACTION2B4 - 348
3X-RAY DIFFRACTION3C4 - 348
4X-RAY DIFFRACTION4D7 - 348

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