[English] 日本語
Yorodumi
- PDB-1ump: GEOMETRY OF TRITERPENE CONVERSION TO PENTACARBOCYCLIC HOPENE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ump
TitleGEOMETRY OF TRITERPENE CONVERSION TO PENTACARBOCYCLIC HOPENE
ComponentsSQUALENE--HOPENE CYCLASE
KeywordsISOMERASE / TRITERPENE CYCLASE / CHOLESTEROL BIOSYNTHESIS / OXIDOSQUALENE CYCLASE / MONOTOPIC MEMBRANE PROTEIN
Function / homology
Function and homology information


squalene-hopanol cyclase / squalene-hopene cyclase / squalene-hopene cyclase activity / lanosterol synthase activity / triterpenoid biosynthetic process / ergosterol biosynthetic process / cholesterol 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
2-AZASQUALENE / Squalene--hopene cyclase
Similarity search - Component
Biological speciesALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsReinert, D.J. / Balliano, G. / Schulz, G.E.
Citation
Journal: Chem.Biol. / Year: 2004
Title: Conversion of Squalene to the Pentacarbocyclic Hopene
Authors: Reinert, D.J. / Balliano, G. / Schulz, G.E.
#1: 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. / Pleschke, A. / Schulz, G.
#2: 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.
#3: Journal: Science / Year: 1997
Title: Structure and Function of a Squalene Cyclase
Authors: Wendt, K.U. / Poralla, K. / Schulz, G.E.
#4: 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 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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)217,72311
Polymers214,9503
Non-polymers2,7738
Water21,7981210
1
A: SQUALENE--HOPENE CYCLASE
hetero molecules

B: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,0477
Polymers143,3002
Non-polymers1,7475
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)145,0477
Polymers143,3002
Non-polymers1,7475
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)145,3538
Polymers143,3002
Non-polymers2,0536
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)139.144, 139.144, 240.699
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(-0.48174, -0.876224, -0.012599), (0.876286, -0.481559, -0.014949), (0.007031, -0.018242, 0.999809)139.94492, -4.8023, 2.45863
2given(-0.532911, 0.84612, -0.009267), (-0.845892, -0.532985, -0.019856), (-0.02174, -0.002743, 0.99976)77.55786, 120.88502, 2.0045
3given(-0.484575, -0.874286, -0.02847), (0.874749, -0.484308, -0.016101), (0.000289, -0.032706, 0.999465)141.24185, -3.81716, -0.64865
DetailsTHE DIMERIC COMPLEX DESCRIBED HERE IS OF THE TYPE A-B', B-A' AND C-C'

-
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.: 5 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-SQA / 2-AZASQUALENE / (4E,8E,12Z,16Z)-N,N,4,8,13,17,21-HEPTAMETHYLDOCOSA-4,8,12,16,20-PENTAEN-1-AMINE


Mass: 413.722 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H51N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1210 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES CYCLIZATION OF SQUALENE TO HOPENE. KEY ENZYME IN HOPANOID (TRITERPENOID) METABOLISM.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 57.84 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: HANGING DROP WITH 5-8 MG/ML PROTEIN,0.3 PERCENT (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 PERCENT (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN ...Details: HANGING DROP WITH 5-8 MG/ML PROTEIN,0.3 PERCENT (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 PERCENT (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN RESPECT TO PROTEIN) 2-AZASQUALENE IN THE STARTING DROPLET. RESERVOIR CONTAINED 100 MM SODIUM CITRATE (PH 4.8), 100 MM SODIUM CHLORIDE, 6-16 PERCENT (V/V) PEG-600.
Crystal grow
*PLUS
Temperature: 20.5 ℃ / pH: 4.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113 mg/mlprotein1drop
2100 mMsodium cirtate1reservoirpH4.8
3100 mM1reservoirNaCl
46-16 %(v/v)PEG6001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98005 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 149921 / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.2
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.13 Å / Lowest resolution: 20 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 4.5 % / Num. unique obs: 11956 / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSZ

1gsz


Resolution: 2.13→19.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.875 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3691 2.5 %RANDOM
Rwork0.186 ---
obs0.187 146229 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.57 Å20 Å2
2---1.14 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.13→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14892 0 195 1210 16297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02115578
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214076
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.95121133
X-RAY DIFFRACTIONr_angle_other_deg0.853332553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69451854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217418
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023462
X-RAY DIFFRACTIONr_nbd_refined0.2040.23563
X-RAY DIFFRACTIONr_nbd_other0.2310.216626
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.28405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.21058
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5191.59222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.933214772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66636356
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6474.56361
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.19 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 271
Rwork0.246 10621
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0336-0.8751-0.38883.41180.93281.83560.13970.07180.3375-0.84350.0682-0.7687-0.15840.1956-0.20790.2846-0.01520.19540.06940.0320.319364.814668.255664.2103
20.83680.1433-0.24391.2473-0.31061.51820.00430.0386-0.0098-0.0470.01720.1249-0.2111-0.1165-0.02150.0810.0563-0.05680.0393-0.04130.059948.077618.208565.8836
34.52320.92071.61620.81440.39931.9381-0.16070.66260.1413-0.15490.11260.0834-0.02390.12320.04810.0767-0.0131-0.00750.11960.00090.0619100.155728.326464.6357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 628
2X-RAY DIFFRACTION2B10 - 628
3X-RAY DIFFRACTION3C10 - 628
Refinement
*PLUS
% reflection Rfree: 2.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

+
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