[English] 日本語
Yorodumi
- PDB-1jof: Neurospora crassa 3-carboxy-cis,cis-mucoante lactonizing enzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jof
TitleNeurospora crassa 3-carboxy-cis,cis-mucoante lactonizing enzyme
ComponentsCARBOXY-CIS,CIS-MUCONATE CYCLASE
KeywordsISOMERASE / BETA-PROPELLER / HOMOTETRAMER / SEMET-PROTEIN
Function / homology
Function and homology information


carboxy-cis,cis-muconate cyclase / carboxy-cis,cis-muconate cyclase activity / 6-phosphogluconolactonase activity / beta-ketoadipate pathway
Similarity search - Function
Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Carboxy-cis,cis-muconate cyclase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKajander, T. / Merckel, M.C. / Thompson, A. / Deacon, A.M. / Mazur, P. / Kozarich, J.W. / Goldman, A.
Citation
Journal: Structure / Year: 2002
Title: The structure of Neurospora crassa 3-carboxy-cis,cis-muconate lactonizing enzyme, a beta propeller cycloisomerase.
Authors: Kajander, T. / Merckel, M.C. / Thompson, A. / Deacon, A.M. / Mazur, P. / Kozarich, J.W. / Goldman, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: 3-Carboxy-cis,cis-muconate lactonizing enzyme from Neurospora crassa: MAD phasing with 80 selenomethionines
Authors: Merckel, M.C. / Kajander, T. / Deacon, A.M. / Thompson, A. / Grossmann, J.G. / Kalkkinen, N. / Goldman, A.
History
DepositionJul 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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: CARBOXY-CIS,CIS-MUCONATE CYCLASE
B: CARBOXY-CIS,CIS-MUCONATE CYCLASE
C: CARBOXY-CIS,CIS-MUCONATE CYCLASE
D: CARBOXY-CIS,CIS-MUCONATE CYCLASE
E: CARBOXY-CIS,CIS-MUCONATE CYCLASE
F: CARBOXY-CIS,CIS-MUCONATE CYCLASE
G: CARBOXY-CIS,CIS-MUCONATE CYCLASE
H: CARBOXY-CIS,CIS-MUCONATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,34734
Polymers333,7238
Non-polymers2,62326
Water12,845713
1
A: CARBOXY-CIS,CIS-MUCONATE CYCLASE
B: CARBOXY-CIS,CIS-MUCONATE CYCLASE
C: CARBOXY-CIS,CIS-MUCONATE CYCLASE
D: CARBOXY-CIS,CIS-MUCONATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,17317
Polymers166,8624
Non-polymers1,31213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: CARBOXY-CIS,CIS-MUCONATE CYCLASE
F: CARBOXY-CIS,CIS-MUCONATE CYCLASE
G: CARBOXY-CIS,CIS-MUCONATE CYCLASE
H: CARBOXY-CIS,CIS-MUCONATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,17317
Polymers166,8624
Non-polymers1,31213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.290, 160.600, 237.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe functional biological unit of CMLE is a hometetramer. The asymmetric unit contains two tetramers.

-
Components

#1: Protein
CARBOXY-CIS,CIS-MUCONATE CYCLASE / E.C.5.5.1.5 / 3-carboxy-cis / cis-muconate lactonizing enzyme / CMLE


Mass: 41715.414 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Production host: Escherichia coli (E. coli)
References: UniProt: P38677, carboxy-cis,cis-muconate cyclase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: PIPES, Ammonium suplhate, beta-mercapto-ethanol, pH 5.7, VAPOR DIFFUSION, SITTING DROP at 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9137, 0.9786, 0.9795, 0.8856
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91371
20.97861
30.97951
40.88561
ReflectionResolution: 2.5→20 Å / Num. all: 122302 / Num. obs: 122302 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 5
Reflection shellResolution: 2.5→2.6 Å / Num. unique all: 0 / Rsym value: 15.6 / % possible all: 75.8
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 75.8 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameClassification
SnBphasing
CCP4model building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 6115 5 %random
Rwork0.212 ---
all-122302 --
obs-122302 92.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22984 0 140 713 23837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.786
X-RAY DIFFRACTIONc_bond_d0.014
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.214 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.8

+
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://pdbjlvh1.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