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- PDB-3g4d: Crystal Structure of (+)-delta-Cadinene Synthase from Gossypium a... -

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Basic information

Entry
Database: PDB / ID: 3g4d
TitleCrystal Structure of (+)-delta-Cadinene Synthase from Gossypium arboreum and Evolutionary Divergence of Metal Binding Motifs for Catalysis
Components(+)-delta-cadinene synthase isozyme XC1
KeywordsLYASE / cyclase / Magnesium / Metal-binding
Function / homology
Function and homology information


(+)-delta-cadinene synthase / (+)-delta-cadinene synthase activity / diterpenoid biosynthetic process / magnesium ion binding
Similarity search - Function
Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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 synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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
BETA-MERCAPTOETHANOL / (+)-delta-cadinene synthase isozyme XC1
Similarity search - Component
Biological speciesGossypium arboreum (tree cotton)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsGennadios, H.A. / Di Costanzo, L. / Miller, D.J. / Allemann, R.K. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal structure of (+)-delta-cadinene synthase from Gossypium arboreum and evolutionary divergence of metal binding motifs for catalysis.
Authors: Gennadios, H.A. / Gonzalez, V. / Di Costanzo, L. / Li, A. / Yu, F. / Miller, D.J. / Allemann, R.K. / Christianson, D.W.
History
DepositionFeb 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 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

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Assembly

Deposited unit
A: (+)-delta-cadinene synthase isozyme XC1
B: (+)-delta-cadinene synthase isozyme XC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0389
Polymers128,4352
Non-polymers6037
Water6,882382
1
A: (+)-delta-cadinene synthase isozyme XC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4524
Polymers64,2181
Non-polymers2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: (+)-delta-cadinene synthase isozyme XC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5865
Polymers64,2181
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.195, 158.195, 158.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein (+)-delta-cadinene synthase isozyme XC1 / D-cadinene synthase XC1


Mass: 64217.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gossypium arboreum (tree cotton) / Production host: Escherichia coli (E. coli) / References: UniProt: Q39761, (+)-delta-cadinene synthase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: drop containing 5 L protein solution (10 mg/mL DCS, 20 mM Tris (pH 8.0), 2 mM MgCl2, 5 mM BME) and 5 L precipitant solution (100 mM Tris (pH 7.5), 200 mM Li2SO4, 15-17% polyethylene glycol ...Details: drop containing 5 L protein solution (10 mg/mL DCS, 20 mM Tris (pH 8.0), 2 mM MgCl2, 5 mM BME) and 5 L precipitant solution (100 mM Tris (pH 7.5), 200 mM Li2SO4, 15-17% polyethylene glycol (PEG) 4000, 100 mM BaCl2 2H2O) was suspended over a reservoir of 600 L precipitant solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 51262 / Num. obs: 51262 / % possible obs: 99.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 19.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 4.65 / Num. unique all: 5144 / Rsym value: 0.525

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Nicotiana tabacum 5-epi aristolochene synthase (PDB ENTRY 5EAT)

5eat


Resolution: 2.403→47.698 Å / SU ML: 0.36 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 2040 3.98 %RANDOM
Rwork0.1918 ---
obs0.1936 51193 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.95 Å2 / ksol: 0.345 e/Å3
Refinement stepCycle: LAST / Resolution: 2.403→47.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8395 0 36 382 8813
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfond_distance0.005
X-RAY DIFFRACTIONfond_angle0.8
X-RAY DIFFRACTIONfihedral_angle16.9
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.403-2.45890.33691140.25593268X-RAY DIFFRACTION99
2.4589-2.52040.29341350.22143280X-RAY DIFFRACTION100
2.5204-2.58850.29211390.2083240X-RAY DIFFRACTION100
2.5885-2.66470.3131270.22813302X-RAY DIFFRACTION100
2.6647-2.75070.30011430.21633235X-RAY DIFFRACTION100
2.7507-2.8490.27531430.21023272X-RAY DIFFRACTION100
2.849-2.9630.2661370.21153260X-RAY DIFFRACTION100
2.963-3.09780.28211310.21643323X-RAY DIFFRACTION100
3.0978-3.26110.28761330.21643268X-RAY DIFFRACTION100
3.2611-3.46540.23751320.20263302X-RAY DIFFRACTION100
3.4654-3.73290.22241450.17473286X-RAY DIFFRACTION100
3.7329-4.10830.2041420.16343281X-RAY DIFFRACTION100
4.1083-4.70240.1721390.15973305X-RAY DIFFRACTION99
4.7024-5.92270.21771530.1713320X-RAY DIFFRACTION100
5.9227-47.7070.22681270.18573211X-RAY DIFFRACTION93

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