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- PDB-6a2d: Crystal structure of a synthase 2 from santalum album in complex ... -

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Basic information

Entry
Database: PDB / ID: 6a2d
TitleCrystal structure of a synthase 2 from santalum album in complex with ligand1
ComponentsSesquisabinene B synthase 2
KeywordsOXIDOREDUCTASE / substrate binding / synthase / inhibitor
Function / homology
Function and homology information


terpene synthase activity / magnesium ion binding
Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Isoprenoid synthase domain superfamily / Terpene cyclase-like 1, C-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpene synthase family, metal binding domain
Sesquisabinene B synthase 2
Biological speciesSantalum album (white sandalwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsHan, X. / Ko, T.P. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
CitationJournal: To be published
Title: Crystal structure of a synthase 2 from santalum album
Authors: Han, X. / Ko, T.P. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sesquisabinene B synthase 2
B: Sesquisabinene B synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,0318
Polymers131,0352
Non-polymers9966
Water15,871881
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-45 kcal/mol
Surface area43430 Å2
Unit cell
γ
α
β
Length a, b, c (Å)132.527, 132.527, 141.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1467-

HOH

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Components

#1: Protein/peptide Sesquisabinene B synthase 2


Mass: 65517.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Santalum album (white sandalwood) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0RCB5
#2: Chemical ChemComp-6R2 / [bis(chloranyl)-[oxidanyl-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]phosphoryl]methyl]phosphonic acid


Mass: 449.243 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H28Cl2O6P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 881 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: AMMONIUM TARTRATE, PEG 3350, MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→25 Å / Num. obs: 90982 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Χ2: 1.025 / Net I/σ(I): 8 / Num. measured all: 606547
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.96-2.036.80.86689730.7350.360.9390.822
2.03-2.116.80.58989690.860.2450.6390.855
2.11-2.216.80.40990170.9250.170.4440.864
2.21-2.326.80.29789720.9620.1230.3220.864
2.32-2.476.70.21190280.980.0880.2290.855
2.47-2.666.70.15490370.9880.0640.1670.875
2.66-2.936.70.09990750.9950.0410.1080.87
2.93-3.356.70.07291300.9970.030.0781.118
3.35-4.226.50.06192090.9970.0260.0662.187
4.22-256.30.02995720.9990.0120.0310.968

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ONG
Resolution: 1.96→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.073 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 4322 4.8 %RANDOM
Rwork0.1782 ---
Obs0.1804 86431 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.31 Å2 / Biso mean: 36.645 Å2 / Biso min: 11.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å2-0 Å2
2--0.64 Å2-0 Å2
3----1.28 Å2
Refinement stepCycle: final / Resolution: 1.96→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8485 0 56 881 9422
Biso mean--40.73 41.82 -
Num. residues----1034
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0110.028819
r_bond_other_d0.0020.028131
r_angle_refined_deg1.5721.95911909
r_angle_other_deg0.9163.00118871
r_dihedral_angle_1_deg6.46251034
r_dihedral_angle_2_deg36.20824.222424
r_dihedral_angle_3_deg15.329151560
r_dihedral_angle_4_deg17.5171550
r_chiral_restr0.1010.21288
r_gen_planes_refined0.0110.0219591
r_gen_planes_other0.0020.021851
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 333 -
Rwork0.272 6263 -
All-6596 -
Obs--100 %

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