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- PDB-5ern: Crystal structure of elongation domain of Phomopsis amygdali fusi... -

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Basic information

Entry
Database: PDB / ID: 5ern
TitleCrystal structure of elongation domain of Phomopsis amygdali fusicoccadiene synthase
ComponentsFusicoccadiene synthaseFusicocca-2,10(14)-diene synthase
KeywordsTRANSFERASE / diterpene synthase / terpenoids / lyase
Function / homology
Function and homology information


fusicocca-2,10(14)-diene synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / isoprenoid biosynthetic process / lyase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fusicoccadiene synthase
Similarity search - Component
Biological speciesPhomopsis amygdali (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.434 Å
AuthorsChen, M. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase.
Authors: Chen, M. / Chou, W.K. / Toyomasu, T. / Cane, D.E. / Christianson, D.W.
History
DepositionNov 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Fusicoccadiene synthase
B: Fusicoccadiene synthase


Theoretical massNumber of molelcules
Total (without water)79,2382
Polymers79,2382
Non-polymers00
Water1,60389
1
A: Fusicoccadiene synthase
B: Fusicoccadiene synthase

A: Fusicoccadiene synthase
B: Fusicoccadiene synthase

A: Fusicoccadiene synthase
B: Fusicoccadiene synthase


Theoretical massNumber of molelcules
Total (without water)237,7156
Polymers237,7156
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area19960 Å2
ΔGint-157 kcal/mol
Surface area73020 Å2
MethodPISA
2
A: Fusicoccadiene synthase

A: Fusicoccadiene synthase

A: Fusicoccadiene synthase


Theoretical massNumber of molelcules
Total (without water)118,8583
Polymers118,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area2810 Å2
ΔGint-23 kcal/mol
Surface area43640 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-35 kcal/mol
Surface area27290 Å2
MethodPISA
4
B: Fusicoccadiene synthase

B: Fusicoccadiene synthase

B: Fusicoccadiene synthase


Theoretical massNumber of molelcules
Total (without water)118,8583
Polymers118,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area2870 Å2
ΔGint-25 kcal/mol
Surface area43660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.867, 104.867, 140.458
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Fusicoccadiene synthase / Fusicocca-2,10(14)-diene synthase / FS / PaDC4:GGS / Geranylgeranyl diphosphate synthase / GGDP synthase / GGS


Mass: 39619.207 Da / Num. of mol.: 2
Fragment: Geranylgeranyl diphosphate synthase, residues 382-719
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phomopsis amygdali (fungus) / Gene: PaFS / Production host: Escherichia coli (E. coli)
References: UniProt: A2PZA5, geranylgeranyl diphosphate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5 M ammonium phosphate, 0.1 M Tris (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 32406 / % possible obs: 95.2 % / Redundancy: 3.2 % / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.434→43.207 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 1626 5.02 %
Rwork0.2226 --
obs0.2252 32390 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.434→43.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 0 89 4708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024719
X-RAY DIFFRACTIONf_angle_d0.6536367
X-RAY DIFFRACTIONf_dihedral_angle_d15.6131791
X-RAY DIFFRACTIONf_chiral_restr0.025723
X-RAY DIFFRACTIONf_plane_restr0.003813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4345-2.50610.36381250.29992505X-RAY DIFFRACTION94
2.5061-2.5870.31121370.27342481X-RAY DIFFRACTION94
2.587-2.67940.3091360.26712529X-RAY DIFFRACTION95
2.6794-2.78670.34911340.27472521X-RAY DIFFRACTION95
2.7867-2.91350.34491300.29322565X-RAY DIFFRACTION96
2.9135-3.06710.37091370.28262559X-RAY DIFFRACTION96
3.0671-3.25920.28161330.27442600X-RAY DIFFRACTION97
3.2592-3.51070.30381430.24942571X-RAY DIFFRACTION95
3.5107-3.86380.26251370.22272567X-RAY DIFFRACTION96
3.8638-4.42240.25931260.19972598X-RAY DIFFRACTION95
4.4224-5.56990.2461550.18542605X-RAY DIFFRACTION96
5.5699-43.21370.23321330.18082663X-RAY DIFFRACTION92

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