[English] 日本語
Yorodumi
- PDB-2sqc: SQUALENE-HOPENE CYCLASE FROM ALICYCLOBACILLUS ACIDOCALDARIUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2sqc
TitleSQUALENE-HOPENE CYCLASE FROM ALICYCLOBACILLUS ACIDOCALDARIUS
ComponentsSQUALENE-HOPENE CYCLASE
KeywordsISOMERASE / TRITERPENE CYCLASE / MONOTOPIC MEMBRANE PROTEIN / QW-SEQUENCE / CHOLESTEROL BIOSYNTHESIS
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 and squalene oxidase repeat / 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 and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Squalene--hopene cyclase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWendt, K.U. / Schulz, G.E.
Citation
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.
#1: Journal: Science / Year: 1997
Title: Structure and Function of a Squalene Cyclase
Authors: Wendt, K.U. / Poralla, K. / Schulz, G.E.
#2: 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.
History
DepositionAug 2, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SQUALENE-HOPENE CYCLASE
B: SQUALENE-HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,0838
Polymers143,2442
Non-polymers1,8396
Water27,2931515
1
A: SQUALENE-HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2353
Polymers71,6221
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SQUALENE-HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8485
Polymers71,6221
Non-polymers1,2264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.820, 118.820, 276.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999, -0.007, 0.054), (0.008, -1, 0.018), (0.054, 0.019, 0.998)
Vector: 114.844, 117.469, -4.2373)

-
Components

#1: Protein SQUALENE-HOPENE CYCLASE


Mass: 71622.031 Da / Num. of mol.: 2 / Mutation: D376C, C435S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Description: THERMOSTABLE, ACIDOPHILIC / Cell line: JM105 / Cellular location: MEMBRANE / Plasmid: PKK223-3 / Species (production host): Escherichia coli / Cell line (production host): JM105 / Cellular location (production host): CYTOPLASMIC MEMBRANE / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12
References: UniProt: P33247, Isomerases; Intramolecular transferases; Transferring other groups
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1515 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMODEL OF THE PROPOSED CATALYTIC BASE IS INDICATED BY ATOM O HOH 1 98.147 29.292 33.208 1.00 28.41

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 65 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
20.3 %(w/v)detergent1drop
350 mMsodium citrate1drop
4100 mMsodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→49 Å / Num. obs: 523124 / % possible obs: 90.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.062 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.146 / % possible all: 59
Reflection
*PLUS
Num. obs: 120483 / Num. measured all: 523124 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 59 % / Num. unique obs: 5694 / Num. measured obs: 9054 / Rmerge(I) obs: 0.146

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SQC

1sqc


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18
Details: INITIAL REFINEMENT USING XPLOR, FOLLOWED BY REFINEMENT USING REFMAC. THE BULK SOLVENT CORRECTION OF X-PLOR USED THROUGHOUT THE REFINEMENT. PRODUCT HOPENE MODELED IN ACTIVE SITE (SEE THE ...Details: INITIAL REFINEMENT USING XPLOR, FOLLOWED BY REFINEMENT USING REFMAC. THE BULK SOLVENT CORRECTION OF X-PLOR USED THROUGHOUT THE REFINEMENT. PRODUCT HOPENE MODELED IN ACTIVE SITE (SEE THE LITERATURE FOR HOPENE NOMENCLATURE) C1 HOP X 13 103.614 31.179 20.850 1.00 20.00 C2 HOP X 13 104.002 31.723 19.469 1.00 20.00 C3 HOP X 13 102.849 32.537 18.869 1.00 20.00 C4 HOP X 13 102.333 33.739 19.747 1.00 20.00 C5 HOP X 13 102.047 33.170 21.166 1.00 20.00 C6 HOP X 13 101.550 34.176 22.155 1.00 20.00 C7 HOP X 13 100.764 33.510 23.240 1.00 20.00 C8 HOP X 13 101.590 32.510 24.080 1.00 20.00 C9 HOP X 13 102.405 31.574 23.074 1.00 20.00 C10 HOP X 13 103.110 32.276 21.878 1.00 20.00 C11 HOP X 13 103.240 30.601 23.915 1.00 20.00 C12 HOP X 13 102.398 29.750 24.828 1.00 20.00 C13 HOP X 13 101.537 30.606 25.808 1.00 20.00 C14 HOP X 13 100.665 31.555 24.953 1.00 20.00 C15 HOP X 13 99.813 32.389 26.001 1.00 20.00 C22 HOP X 13 99.698 30.849 30.226 1.00 20.00 C23 HOP X 13 103.398 34.803 19.717 1.00 20.00 C24 HOP X 13 101.099 34.259 19.068 1.00 20.00 C25 HOP X 13 104.383 33.039 22.288 1.00 20.00 C26 HOP X 13 102.570 33.339 24.968 1.00 20.00 C27 HOP X 13 99.678 30.771 24.088 1.00 20.00 C28 HOP X 13 100.156 28.456 26.313 1.00 20.00 C29 HOP X 13 98.842 29.609 30.376 1.00 20.00 C30 HOP X 13 99.828 31.851 31.405 1.00 20.00
RfactorNum. reflection% reflectionSelection details
Rfree0.187 6059 5.3 %RANDOM
Rwork0.153 ---
obs-114164 90 %-
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9988 0 126 1515 11629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d2.2
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / Rfactor Rfree: 0.239 / Num. reflection Rwork: 4807 / Rfactor obs: 0.196

+
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