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- PDB-6a1e: Crystal structure of a synthase 1 from Santalum album in complex ... -

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Basic information

Entry
Database: PDB / ID: 6a1e
TitleCrystal structure of a synthase 1 from Santalum album in complex with ligand fps
ComponentsSesquisabinene B synthase 1
KeywordsTRANSFERASE / ligand synthase
Function / homology
Function and homology information


diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase ...Terpene cyclase-like 1, C-terminal domain / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBONATE ION / Chem-FPS / Sesquisabinene B synthase 1
Similarity search - Component
Biological speciesSantalum album (white sandalwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHan, X. / Ko, T.P. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: To Be Published
Title: Crystal structure of a synthase 1 from Santalum album in complex with ligand
Authors: Han, X. / Ko, T.P. / Liu, W.D. / Chen, C.C. / Guo, R.T.
History
DepositionJun 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 2.0Sep 2, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn / entity / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules ..._diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _software.classification / _software.name / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_site.pdbx_num_residues
Description: Model completeness
Details: The overall structure is not changed, we re-refined the structure according to a reviewer of our manuscript referring to this structure, we got better bond length and bond angle parameter, ...Details: The overall structure is not changed, we re-refined the structure according to a reviewer of our manuscript referring to this structure, we got better bond length and bond angle parameter, and deleted some distant waters.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Sesquisabinene B synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,54011
Polymers65,2951
Non-polymers1,24510
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-52 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.611, 139.498, 110.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1017-

HOH

21A-1212-

HOH

31A-1214-

HOH

41A-1215-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sesquisabinene B synthase 1


Mass: 65294.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Santalum album (white sandalwood) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2(DE3) / References: UniProt: A0A0A0RDR2

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Non-polymers , 6 types, 426 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O6P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.33 % / Mosaicity: 0.415 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium Sulfate, HEPES, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2016
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→25 Å / Num. obs: 53005 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Rrim(I) all: 0.04 / Χ2: 1.348 / Net I/σ(I): 13.2 / Num. measured all: 503665
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.491 / Num. unique obs: 8989 / CC1/2: 1 / Rpim(I) all: 0.007 / Rrim(I) all: 0.017 / Χ2: 0.729 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ONG

2ong


Resolution: 1.89→24.32 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.828 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 2547 5 %RANDOM
Rwork0.1538 ---
obs0.156 48463 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.63 Å2 / Biso mean: 35.257 Å2 / Biso min: 16.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 1.89→24.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 73 416 4678
Biso mean--73.46 43.68 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174114
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.6446108
X-RAY DIFFRACTIONr_angle_other_deg1.4011.5839534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03522.579252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24315773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2621528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02987
LS refinement shellResolution: 1.891→1.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 152 -
Rwork0.233 3204 -
all-3356 -
obs--86.52 %

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