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- PDB-1di1: CRYSTAL STRUCTURE OF ARISTOLOCHENE SYNTHASE FROM PENICILLIUM ROQU... -

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Basic information

Entry
Database: PDB / ID: 1di1
TitleCRYSTAL STRUCTURE OF ARISTOLOCHENE SYNTHASE FROM PENICILLIUM ROQUEFORTI
ComponentsARISTOLOCHENE SYNTHASE
KeywordsLYASE / SESQUITERPENE CYCLASE / ISOPRENOID BIOSYNTHESIS
Function / homology
Function and homology information


aristolochene synthase / aristolochene synthase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Aristolochene synthase
Similarity search - Component
Biological speciesPenicillium roqueforti (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsCaruthers, J.M. / Kang, I. / Cane, D.E. / Christianson, D.W. / Rynkiewicz, M.J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure determination of aristolochene synthase from the blue cheese mold, Penicillium roqueforti.
Authors: Caruthers, J.M. / Kang, I. / Rynkiewicz, M.J. / Cane, D.E. / Christianson, D.W.
History
DepositionNov 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: ARISTOLOCHENE SYNTHASE
B: ARISTOLOCHENE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)68,9942
Polymers68,9942
Non-polymers00
Water5,963331
1
A: ARISTOLOCHENE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)34,4971
Polymers34,4971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ARISTOLOCHENE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)34,4971
Polymers34,4971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.200, 208.200, 139.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein ARISTOLOCHENE SYNTHASE / / SESQUITERPENE CYCLASE / AS


Mass: 34497.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium roqueforti (fungus) / Plasmid: PZW04 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03471, EC: 4.1.99.7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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

Crystal
*PLUS
Density % sol: 72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.5M NACL, 4% PEG6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 %PEG60001reservoir
20.5 M1reservoirNaCl
313 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.71069
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71069 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 166088 / Num. obs: 46972 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.395 / % possible all: 86
Reflection
*PLUS
Num. measured all: 166088
Reflection shell
*PLUS
% possible obs: 86 %

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Processing

Software
NameClassification
PHASESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.273 4420 RANDOM
Rwork0.247 --
all0.248 43895 -
obs0.248 39475 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 0 331 5023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d0.03
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.76
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_deg18.8
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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