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- PDB-3s9v: abietadiene synthase from Abies grandis -

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Basic information

Entry
Database: PDB / ID: 3s9v
Titleabietadiene synthase from Abies grandis
ComponentsAbietadiene synthase, chloroplastic
KeywordsLyase / isomerase / Alpha bundle/barrel
Function / homology
Function and homology information


neoabietadiene synthase / abieta-7,13-diene synthase / abietadiene synthase activity / copalyl diphosphate synthase activity / copalyl diphosphate synthase / terpene synthase activity / metabolic process / chloroplast / magnesium ion binding
Similarity search - Function
Glycosyltransferase - #160 / 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 - #160 / 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
Bifunctional abietadiene synthase, chloroplastic
Similarity search - Component
Biological speciesAbies grandis (grand fir)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 2.3 Å
AuthorsZhou, K. / Hoy, J.A. / Mann, F.M. / Honzatko, R.B. / Peters, R.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Insights into diterpene cyclization from structure of bifunctional abietadiene synthase from Abies grandis.
Authors: Zhou, K. / Gao, Y. / Hoy, J.A. / Mann, F.M. / Honzatko, R.B. / Peters, R.J.
History
DepositionJun 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abietadiene synthase, chloroplastic
B: Abietadiene synthase, chloroplastic
C: Abietadiene synthase, chloroplastic
D: Abietadiene synthase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)364,3464
Polymers364,3464
Non-polymers00
Water23,9061327
1
A: Abietadiene synthase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)91,0871
Polymers91,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Abietadiene synthase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)91,0871
Polymers91,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Abietadiene synthase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)91,0871
Polymers91,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Abietadiene synthase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)91,0871
Polymers91,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.840, 189.085, 99.895
Angle α, β, γ (deg.)90.000, 91.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Abietadiene synthase, chloroplastic / (-)-abieta-7(8) / 13(14)-diene synthase / Abietadiene cyclase / Agggabi / Abietadiene synthase / ...(-)-abieta-7(8) / 13(14)-diene synthase / Abietadiene cyclase / Agggabi / Abietadiene synthase / Copalyl diphosphate synthase


Mass: 91086.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Abies grandis (grand fir) / Gene: ag22, ac22 / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q38710, abieta-7,13-diene synthase, copalyl diphosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1327 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 25% PEG 8000, 0.1 M sodium citrate, 0.1 M ammonium dibasic phosphate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Av σ(I) over netI: 18.46 / Number: 271627 / Rmerge(I) obs: 0.104 / Χ2: 3.72 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 61432 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.785092.210.08616.6144.2
5.386.7810010.09411.1374.7
4.75.3899.810.0716.7154.6
4.274.799.910.0665.3124.4
3.974.2799.910.0724.5194.5
3.733.9710010.0823.864.6
3.553.7310010.0923.3414.6
3.393.5599.910.1042.7664.6
3.263.3910010.1162.2684.5
3.153.2610010.1392.1284.5
3.053.1510010.1551.7634.4
2.963.0599.610.1961.6924.4
2.892.9699.710.2441.5844.3
2.822.8999.810.2951.4584.3
2.752.8299.510.3411.424.3
2.692.7599.110.3821.3284.3
2.642.6998.910.4621.314.3
2.592.6498.710.5651.264.3
2.542.5998.610.6111.1974.2
2.52.5498.410.7391.5244.3
ReflectionResolution: 2.3→50 Å / Num. obs: 148465 / % possible obs: 97.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.092 / Χ2: 2.048 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3430.3673411.186196.6
2.34-2.383.10.33173461.228196.7
2.38-2.433.20.3173031.161196.7
2.43-2.483.20.27174011.232197.8
2.48-2.533.20.24874571.236198.4
2.53-2.593.20.22375091.323199.1
2.59-2.663.20.275611.355199.4
2.66-2.733.20.18375541.457199.3
2.73-2.813.30.1675191.598199.2
2.81-2.93.30.14675101.77199.1
2.9-33.30.12475271.892198.9
3-3.123.30.10774742.027198.7
3.12-3.263.30.08974582.098198.9
3.26-3.443.30.07775452.263198.3
3.44-3.653.20.06974352.469198.2
3.65-3.933.20.06973863.205197.3
3.93-4.333.20.0673963.404197.1
4.33-4.953.20.05273693.189196.3
4.95-6.243.10.05772793.44195.2
6.24-5030.04870953.643192

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MRRfactor: 35.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å45.95 Å
Translation2.3 Å45.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Occupancy max: 1 / Occupancy min: 0.35 / Isotropic thermal model: overall / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 14818 9.7 %random
Rwork0.1974 ---
all-152264 --
obs-148289 97.4 %-
Solvent computationBsol: 34.1245 Å2
Displacement parametersBiso max: 120.09 Å2 / Biso mean: 34.3214 Å2 / Biso min: 2.65 Å2
Baniso -1Baniso -2Baniso -3
1--8.508 Å20 Å20.334 Å2
2---9.056 Å20 Å2
3---17.564 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24754 0 0 1327 26081
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.3492
X-RAY DIFFRACTIONc_scbond_it5.4834
X-RAY DIFFRACTIONc_mcangle_it3.6634
X-RAY DIFFRACTIONc_scangle_it7.566
LS refinement shellResolution: 2.3→2.32 Å
RfactorNum. reflection
Rfree0.339 281
Rwork0.29 -
obs-2350
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param \par
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param \par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param \par

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