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- PDB-4okz: Selinadiene Synthase in complex with dihydrofarnesyl pyrophosphate -

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Basic information

Entry
Database: PDB / ID: 4okz
TitleSelinadiene Synthase in complex with dihydrofarnesyl pyrophosphate
ComponentsTerpene synthase metal-binding domain-containing protein
KeywordsTRANSFERASE / Sesquiterpene / cyclase / terpenoid / induced fit / closed conformation / Dihydrofarnesyl pyrophosphate / 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
Chem-3E9 / 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: 1.9 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 23, 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 1.3Aug 20, 2014Group: Non-polymer description
Revision 1.4Sep 20, 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 / 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

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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)166,96320
Polymers165,1344
Non-polymers1,82916
Water21,4201189
1
A: Terpene synthase metal-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7415
Polymers41,2831
Non-polymers4574
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)41,7415
Polymers41,2831
Non-polymers4574
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)41,7415
Polymers41,2831
Non-polymers4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Terpene synthase metal-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7415
Polymers41,2831
Non-polymers4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.090, 117.780, 185.590
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(-0.859515, -0.014125, -0.510915), (-0.011931, -0.998791, 0.047684), (-0.510971, 0.047081, 0.858307)-142.349, 228.82031, -44.95384
3given(-0.78283, 0.369452, 0.500681), (0.378574, 0.921381, -0.087973), (-0.49382, 0.120677, -0.86115)-195.22859, 39.05011, -27.95064
4given(0.921699, -0.387713, 0.012254), (-0.387832, -0.920442, 0.048706), (-0.007605, -0.049644, -0.998738)38.85039, 191.4568, 33.46207

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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.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-3E9 / (3S,6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl trihydrogen diphosphate


Mass: 384.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
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 dihydrofarnesyl 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 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2013
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 130090 / Num. obs: 129570 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.8
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6

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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: PDB entry 4OKM

4okm


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.487 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17711 6479 5 %RANDOM
Rwork0.14272 ---
obs0.14446 123091 99.57 %-
all-129570 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-0 Å2
2--2.74 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11006 0 108 1189 12303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911430
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210614
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.95815490
X-RAY DIFFRACTIONr_angle_other_deg0.8693.00324306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.72951378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65722.887568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.373151788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.85315120
X-RAY DIFFRACTIONr_chiral_restr0.0690.21682
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022726
X-RAY DIFFRACTIONr_rigid_bond_restr1.414322044
X-RAY DIFFRACTIONr_sphericity_free27.8945337
X-RAY DIFFRACTIONr_sphericity_bonded7.455522587
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 466 -
Rwork0.193 8852 -
obs--99.47 %
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)
10.10290.02270.01550.08180.00890.11810.00430.00880.00010.00640.0056-0.01150.00110.0311-0.00990.00060.0002-0.00140.0342-0.00520.0126-72.2792118.384542.8393
20.0627-0.01020.00420.07570.02270.12260.0019-0.001-0.00140.0003-0.00110.00190.0105-0.0242-0.00080.0084-0.00490.00070.0289-0.00180.0094-103.7678113.471534.2625
30.07580.00920.00640.0471-0.0010.18030.0051-0.00180.0047-0.0029-0.00140.0042-0.0322-0.0197-0.00370.01770.00490.00310.0227-0.00050.007-101.1844127.0263-6.3592
40.0769-0.0074-0.05310.08080.0210.15820.0023-0.01120.00120.00020.0056-0.0120.01360.0316-0.0080.00880.0061-0.00090.0306-0.0020.0084-74.1716109.8632-14.2956
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 DIFFRACTION4D4 - 349

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