[English] 日本語
Yorodumi
- PDB-1gsz: Crystal Structure of a Squalene Cyclase in Complex with the Poten... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gsz
TitleCrystal Structure of a Squalene Cyclase in Complex with the Potential Anticholesteremic Drug Ro48-8071
ComponentsSQUALENE--HOPENE CYCLASE
KeywordsISOMERASE / CHOLESTEROL BIOSYNTHESIS / INHIBITOR OXIDOSQUALENE CYCLASE / MONOTOPIC MEMBRANE PROTEIN
Function / homology
Function and homology information


squalene-hopanol cyclase / squalene-hopene cyclase / squalene-hopene cyclase activity / triterpenoid biosynthetic process / lipid droplet / lyase activity / plasma membrane
Similarity search - Function
Squalene hopene cyclase / Terpene synthase, conserved site / Terpene synthases signature. / Squalene cyclase, N-terminal / Squalene-hopene cyclase N-terminal domain / Squalene cyclase / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 ...Squalene hopene cyclase / Terpene synthase, conserved site / Terpene synthases signature. / Squalene cyclase, N-terminal / Squalene-hopene cyclase N-terminal domain / Squalene cyclase / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Chem-R71 / Squalene--hopene cyclase
Similarity search - Component
Biological speciesALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.8 Å
AuthorsLenhart, A. / Weihofen, W.A. / Pleschke, A.E.W. / Schulz, G.E.
Citation
Journal: Chem.Biol. / Year: 2002
Title: Crystal Structure of a Squalene Cyclase in Complex with the Potential Anticholesteremic Drug Ro48-8071
Authors: Lenhart, A. / Weihofen, W.A. / Pleschke, A.E.W. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The Structure of the Membrane Protein Squalene-Hopene Cyclase at 2.0 A Resolution
Authors: Wendt, K.U. / Lenhart, A. / Schulz, G.E.
#2: Journal: Science / Year: 1997
Title: Structure and Function of a Squalene Cyclase
Authors: Wendt, K.U. / Poralla, K. / Schulz, G.E.
#3: Journal: Protein Sci. / Year: 1997
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Squalene-Hopene Cyclase from Alicyclobacillus Acidocaldarius
Authors: Wendt, K.U. / Feil, C. / Lenhart, A. / Poralla, K. / Schulz, G.E.
#4: Journal: J.Lipid Res. / Year: 1997
Title: Ro48-8071, a New 2,3-Oxidosqualene:Lanosterol Cyclase Inhibitor Lowering Plasma Cholesterol in Hamsters, Squirrel Monkeys, and Minipigs: Comparison to Simvastatin
Authors: Morand, O.H. / Aebi, J.D. / Dehmlow, H. / Ji, Y.H. / Gains, N. / Lengsfeld, H. / Himber, J.
History
DepositionJan 9, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SQUALENE--HOPENE CYCLASE
B: SQUALENE--HOPENE CYCLASE
C: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,2159
Polymers214,9503
Non-polymers2,2646
Water4,594255
1
A: SQUALENE--HOPENE CYCLASE
hetero molecules

B: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8106
Polymers143,3002
Non-polymers1,5104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
MethodPQS
2
B: SQUALENE--HOPENE CYCLASE
hetero molecules

A: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8106
Polymers143,3002
Non-polymers1,5104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+2/31
MethodPQS
3
C: SQUALENE--HOPENE CYCLASE
hetero molecules

C: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8106
Polymers143,3002
Non-polymers1,5104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)140.897, 140.897, 244.049
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.484541, -0.874759, -0.004148), (0.874768, -0.484542, -0.000834), (-0.001281, -0.004033, 0.999991)141.123, -5.245, 1.529
2given(-0.529047, 0.848507, -0.012053), (-0.848531, -0.529126, -0.004461), (-0.010162, 0.007867, 0.999917)77.886, 121.444, 0.369
3given(-0.485848, -0.873918, -0.014797), (0.874022, -0.485884, -0.001242), (-0.006104, -0.013536, 0.99989)141.88901, -4.447, -0.369

-
Components

#1: Protein SQUALENE--HOPENE CYCLASE


Mass: 71650.039 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
Description: THERMOSTABLE, ACIDOPHILIC / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): JM105 / References: UniProt: P33247, squalene-hopene cyclase
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-R71 / [4-({6-[ALLYL(METHYL)AMINO]HEXYL}OXY)-2-FLUOROPHENYL](4-BROMOPHENYL)METHANONE / Ro 48-8071


Mass: 448.368 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H27BrFNO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE CREATION OF HOPENE BY CYCLIZATION OF SQUALENE.
Sequence detailsMET 1 IS NOT IN SWISS-PROT ENTRY. RESIDUES UP TO ALA 10 AND AFTER ILE 628 HAVE NO ELECTRON DENSITY ...MET 1 IS NOT IN SWISS-PROT ENTRY. RESIDUES UP TO ALA 10 AND AFTER ILE 628 HAVE NO ELECTRON DENSITY (ALL PDB-NUMBERING).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: HANGING DROP WITH 5...8 MG/ML PROTEIN, 0.3 % (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 % (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN RESPECT TO ...Details: HANGING DROP WITH 5...8 MG/ML PROTEIN, 0.3 % (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 % (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN RESPECT TO PROTEIN) RO48-8071 IN THE STARTING DROPLET. RESERVOIR CONTAINED 100 MM SODIUM CITRATE (PH 4.8), 100 MM SODIUM CHLORIDE, 6...16 % (V/V) PEG-600.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15-8 mg/mlSHC1drop
20.3 %(w/v)C8E41reservoir
350 mM1reservoirNaCl
450 mMsodium citrate1reservoirpH4.8
53-8 %(v/v)satPEG6001reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: SIEMENS MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 54249 / % possible obs: 78.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.4 / % possible all: 47.6
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 79 % / Num. measured all: 156593 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 48 %

-
Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.8→25 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1989 2.9 %RANDOM
Rwork0.203 ---
obs0.203 54200 78 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0971 Å2 / ksol: 0.259545 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å24.68 Å20 Å2
2---2.15 Å20 Å2
3---4.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14892 0 147 255 15294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 206 3.8 %
Rwork0.384 5234 -
obs--47.7 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 3.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

+
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