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- PDB-5imi: Crystal structure of S303A Aspergillus terreus aristolochene synt... -

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Basic information

Entry
Database: PDB / ID: 5imi
TitleCrystal structure of S303A Aspergillus terreus aristolochene synthase complexed with (1S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)decahydroquinolizin-5-ium
ComponentsAristolochene synthase
KeywordsLYASE/LYASE INHIBITOR / Lyase / terpene cyclases / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


aristolochene synthase / aristolochene synthase activity / isoprenoid biosynthetic process / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / 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
Chem-JF1 / PYROPHOSPHATE 2- / Aristolochene synthase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.462 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: Biochemistry / Year: 2016
Title: Probing the Role of Active Site Water in the Sesquiterpene Cyclization Reaction Catalyzed by Aristolochene Synthase.
Authors: Chen, M. / Chou, W.K. / Al-Lami, N. / Faraldos, J.A. / Allemann, R.K. / Cane, D.E. / Christianson, D.W.
History
DepositionMar 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _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 1.4Sep 27, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aristolochene synthase
B: Aristolochene synthase
C: Aristolochene synthase
D: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,74325
Polymers144,8224
Non-polymers1,92121
Water10,845602
1
A: Aristolochene synthase
hetero molecules

B: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,41713
Polymers72,4112
Non-polymers1,00711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z+1/31
Buried area3170 Å2
ΔGint-68 kcal/mol
Surface area25020 Å2
2
C: Aristolochene synthase
hetero molecules

D: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,32512
Polymers72,4112
Non-polymers91410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y,x-1,-z1
Buried area3340 Å2
ΔGint-69 kcal/mol
Surface area25110 Å2
3
B: Aristolochene synthase
D: Aristolochene synthase
hetero molecules

A: Aristolochene synthase
hetero molecules

C: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,74325
Polymers144,8224
Non-polymers1,92121
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x+y,-x-1,z-1/31
crystal symmetry operation4_655y+1,x,-z1
Buried area9460 Å2
ΔGint-137 kcal/mol
Surface area47170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.127, 124.127, 203.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aristolochene synthase / AS / Sesquiterpene cyclase


Mass: 36205.395 Da / Num. of mol.: 4 / Mutation: S303A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: Ari1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UR08, aristolochene synthase

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Non-polymers , 5 types, 623 molecules

#2: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-JF1 / (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium


Mass: 208.363 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H26N
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 200 mM ammonium acetate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 66366 / % possible obs: 100 % / Redundancy: 13.9 % / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
PHENIXdev_1803refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KUX

4kux


Resolution: 2.462→47.521 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.88
RfactorNum. reflection% reflection
Rfree0.2505 2003 3.02 %
Rwork0.2122 --
obs0.2134 66303 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.462→47.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9857 0 114 602 10573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210210
X-RAY DIFFRACTIONf_angle_d0.58313845
X-RAY DIFFRACTIONf_dihedral_angle_d14.4993864
X-RAY DIFFRACTIONf_chiral_restr0.0281520
X-RAY DIFFRACTIONf_plane_restr0.0031769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4616-2.52320.35271440.29324514X-RAY DIFFRACTION100
2.5232-2.59140.33321430.2764579X-RAY DIFFRACTION100
2.5914-2.66770.34881390.2784491X-RAY DIFFRACTION100
2.6677-2.75380.31861370.26294555X-RAY DIFFRACTION100
2.7538-2.85220.3261450.24624538X-RAY DIFFRACTION100
2.8522-2.96640.35371440.264569X-RAY DIFFRACTION100
2.9664-3.10130.27561410.25194549X-RAY DIFFRACTION100
3.1013-3.26480.27011430.24014589X-RAY DIFFRACTION100
3.2648-3.46930.27441390.23024550X-RAY DIFFRACTION100
3.4693-3.73710.25631410.22034592X-RAY DIFFRACTION100
3.7371-4.1130.22981410.18824636X-RAY DIFFRACTION100
4.113-4.70760.22241430.17734620X-RAY DIFFRACTION100
4.7076-5.92930.23251510.19434679X-RAY DIFFRACTION100
5.9293-47.52960.16291520.15954839X-RAY DIFFRACTION100

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