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- PDB-3g4f: Crystal Structure of (+)- -Cadinene Synthase from Gossypium arbor... -

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Basic information

Entry
Database: PDB / ID: 3g4f
TitleCrystal Structure of (+)- -Cadinene Synthase from Gossypium arboreum in complex with 2-fluorofarnesyl diphosphate
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 / Chem-FPF / (+)-delta-cadinene synthase isozyme XC1
Similarity search - Component
Biological speciesGossypium arboreum (tree cotton)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsGennadios, H.A. / Di Costanzo, L. / 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 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: (+)-delta-cadinene synthase isozyme XC1
B: (+)-delta-cadinene synthase isozyme XC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,53812
Polymers128,4352
Non-polymers1,10310
Water3,171176
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A: (+)-delta-cadinene synthase isozyme XC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8477
Polymers64,2181
Non-polymers6296
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)64,6915
Polymers64,2181
Non-polymers4734
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.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-FPF / (2Z,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 400.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H27FO7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 7.5
Details: crystals of unliganded DCS were gradually transferred to a stabilizing solution containing 100 mM Tris (pH 7.5), 200 mM Li2SO4, 17-19% PEG 4000, 2 mM 2F-FPP and allowed to soak for 16 hours. ...Details: crystals of unliganded DCS were gradually transferred to a stabilizing solution containing 100 mM Tris (pH 7.5), 200 mM Li2SO4, 17-19% PEG 4000, 2 mM 2F-FPP and allowed to soak for 16 hours. Crystals were slowly cryoprotected with stabilizing solution containing 2 mM MnCl2 and 25% glycerol and then flash cooled with liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.651→50 Å / Num. obs: 38457 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 2.651→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.487 / % possible all: 99.9

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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: The unliganded structure

Resolution: 2.651→47.698 Å / SU ML: 0.83 / σ(F): 1.35 / Phase error: 33.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 3013 7.83 %
Rwork0.2013 --
obs0.2064 38457 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.288 Å2 / ksol: 0.331 e/Å3
Refinement stepCycle: LAST / Resolution: 2.651→47.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8418 0 64 176 8658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018666
X-RAY DIFFRACTIONf_angle_d1.34111718
X-RAY DIFFRACTIONf_dihedral_angle_d21.3823178
X-RAY DIFFRACTIONf_chiral_restr0.0871260
X-RAY DIFFRACTIONf_plane_restr0.0061502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.651-2.692100.28141723X-RAY DIFFRACTION99
2.6921-2.736200.26641716X-RAY DIFFRACTION100
2.7362-2.783400.27491724X-RAY DIFFRACTION100
2.7834-2.83400.26711740X-RAY DIFFRACTION100
2.834-2.88850.3382450.26111704X-RAY DIFFRACTION100
2.8885-2.94740.32931980.24551559X-RAY DIFFRACTION100
2.9474-3.01150.29731630.25741528X-RAY DIFFRACTION100
3.0115-3.08160.35441710.25641573X-RAY DIFFRACTION100
3.0816-3.15860.2941780.25181565X-RAY DIFFRACTION100
3.1586-3.2440.29761590.23841567X-RAY DIFFRACTION100
3.244-3.33940.34311630.23691604X-RAY DIFFRACTION100
3.3394-3.44720.30161430.21711561X-RAY DIFFRACTION100
3.4472-3.57040.26181740.20241583X-RAY DIFFRACTION100
3.5704-3.71330.24791770.1781556X-RAY DIFFRACTION100
3.7133-3.88220.21591710.19291596X-RAY DIFFRACTION100
3.8822-4.08680.23451750.17571559X-RAY DIFFRACTION100
4.0868-4.34260.23481790.17271567X-RAY DIFFRACTION100
4.3426-4.67770.23142060.15921571X-RAY DIFFRACTION100
4.6777-5.14790.23341840.16181576X-RAY DIFFRACTION100
5.1479-5.89160.26171750.18161610X-RAY DIFFRACTION100
5.8916-7.41840.28531750.19871601X-RAY DIFFRACTION100
7.4184-47.70620.19411770.15851661X-RAY DIFFRACTION99

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