[English] 日本語
Yorodumi
- PDB-4kux: Crystal structure of Aspergillus terreus aristolochene synthase c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kux
TitleCrystal structure of Aspergillus terreus aristolochene synthase complexed with farnesyl thiolodiphosphate (FSPP)
ComponentsAristolochene synthase
KeywordsLYASE / Class I terpene cyclase
Function / homology
Function and homology information


aristolochene synthase / aristolochene synthase activity / 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-FPS / Aristolochene synthase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, M. / Faraldos, J.A. / Al-lami, N. / Janvier, M. / D'Antonio, E.L. / Cane, D.E. / Allemann, R.K. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2013
Title: Mechanistic insights from the binding of substrate and carbocation intermediate analogues to aristolochene synthase.
Authors: Chen, M. / Al-Lami, N. / Janvier, M. / D'Antonio, E.L. / Faraldos, J.A. / Cane, D.E. / Allemann, R.K. / Christianson, D.W.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)146,95522
Polymers144,8864
Non-polymers2,06918
Water17,619978
1
A: Aristolochene synthase
B: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,47711
Polymers72,4432
Non-polymers1,0359
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-86 kcal/mol
Surface area24970 Å2
MethodPISA
2
C: Aristolochene synthase
D: Aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,47711
Polymers72,4432
Non-polymers1,0359
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-84 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.952, 123.952, 203.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Aristolochene synthase / AS / Sesquiterpene cyclase


Mass: 36221.395 Da / Num. of mol.: 4 / Fragment: UNP residues 14-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: Ari1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9UR08, aristolochene synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H28O6P2S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3 uL protein (10 mg/mL ATAS, 20 mM MES, pH 6.5, 1.9 mM magnesium chloride, 120 mM sodium chloride, 3 mM BME, 1.5 mM FSPP) + 3 uL precipitant (200 mM magnesium acetate, 17% PEG3350) against ...Details: 3 uL protein (10 mg/mL ATAS, 20 mM MES, pH 6.5, 1.9 mM magnesium chloride, 120 mM sodium chloride, 3 mM BME, 1.5 mM FSPP) + 3 uL precipitant (200 mM magnesium acetate, 17% PEG3350) against 500 uL precipitant, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2012
Details: Cryogenically cooled double crystal monochromator with horizontally focusing sagitally bent second crystal with 4:1 magnification ratio and vertically focusing mirror
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 142435 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 30.375
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.522 / % possible all: 100

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASER(CCP4)phasing
PHENIX(phenix.refine: dev_1370)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KVD

4kvd


Resolution: 1.9→50 Å / SU ML: 0.24 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 7147 5.02 %RANDOM
Rwork0.1893 ---
obs0.1893 142431 99.9 %-
all-142534 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9816 0 120 978 10914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410156
X-RAY DIFFRACTIONf_angle_deg1.413745
X-RAY DIFFRACTIONf_dihedral_angle_d20.93835
X-RAY DIFFRACTIONf_improper_angle_d2.181491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92180.34812430.31234419X-RAY DIFFRACTION99
1.9218-1.94440.35432280.29214447X-RAY DIFFRACTION100
1.9444-1.96810.30252320.27244505X-RAY DIFFRACTION100
1.9681-1.9930.30772300.25364449X-RAY DIFFRACTION100
1.993-2.01920.26712490.24434461X-RAY DIFFRACTION100
2.0192-2.04690.30862230.23334434X-RAY DIFFRACTION100
2.0469-2.07610.27352460.22614499X-RAY DIFFRACTION100
2.0761-2.10710.28332340.22854477X-RAY DIFFRACTION100
2.1071-2.140.26842080.21964506X-RAY DIFFRACTION100
2.14-2.17510.25922180.21514493X-RAY DIFFRACTION100
2.1751-2.21260.27872400.21764491X-RAY DIFFRACTION100
2.2126-2.25290.27032560.21334448X-RAY DIFFRACTION100
2.2529-2.29620.27322590.20924471X-RAY DIFFRACTION100
2.2962-2.34310.25692380.19964490X-RAY DIFFRACTION100
2.3431-2.3940.25782500.1934447X-RAY DIFFRACTION100
2.394-2.44970.22492280.19144506X-RAY DIFFRACTION100
2.4497-2.5110.25522450.19754472X-RAY DIFFRACTION100
2.511-2.57880.24462310.19864504X-RAY DIFFRACTION100
2.5788-2.65470.22062550.20374492X-RAY DIFFRACTION100
2.6547-2.74040.23582390.2024503X-RAY DIFFRACTION100
2.7404-2.83830.2392380.20294516X-RAY DIFFRACTION100
2.8383-2.9520.25792370.21014508X-RAY DIFFRACTION100
2.952-3.08630.24092420.21244527X-RAY DIFFRACTION100
3.0863-3.2490.23542240.20274532X-RAY DIFFRACTION100
3.249-3.45250.23712430.19784536X-RAY DIFFRACTION100
3.4525-3.71890.21512620.18274516X-RAY DIFFRACTION100
3.7189-4.0930.19522400.15864559X-RAY DIFFRACTION100
4.093-4.68480.16432380.13934599X-RAY DIFFRACTION100
4.6848-5.90060.18082340.16064647X-RAY DIFFRACTION100
5.9006-47.48980.17092370.15474830X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more