[English] 日本語
Yorodumi
- PDB-1yfm: RECOMBINANT YEAST FUMARASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yfm
TitleRECOMBINANT YEAST FUMARASE
ComponentsFUMARASE
KeywordsLYASE / FUMARASE / KREBS CYCLE / ACTIVE SITE WATER / HYDRATASE / MULTI-SUBUNIT ACTIVE SITE
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / Mitochondrial protein degradation / tricarboxylic acid cycle / double-strand break repair / mitochondrial matrix / DNA damage response ...Citric acid cycle (TCA cycle) / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / Mitochondrial protein degradation / tricarboxylic acid cycle / double-strand break repair / mitochondrial matrix / DNA damage response / mitochondrion / nucleus / cytosol
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fumarate hydratase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWeaver, T.M. / Lees, M.R. / Banaszak, L.J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crystal structures of native and recombinant yeast fumarase.
Authors: Weaver, T. / Lees, M. / Zaitsev, V. / Zaitseva, I. / Duke, E. / Lindley, P. / McSweeny, S. / Svensson, A. / Keruchenko, J. / Keruchenko, I. / Gladilin, K. / Banaszak, L.
History
DepositionJan 7, 1998Processing site: BNL
Revision 1.0Jul 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
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: FUMARASE


Theoretical massNumber of molelcules
Total (without water)53,2451
Polymers53,2451
Non-polymers00
Water00
1
A: FUMARASE

A: FUMARASE

A: FUMARASE

A: FUMARASE


Theoretical massNumber of molelcules
Total (without water)212,9794
Polymers212,9794
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation7_558y,x,-z+31
crystal symmetry operation8_778-y+2,-x+2,-z+31
Buried area27450 Å2
ΔGint-149 kcal/mol
Surface area57590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.190, 95.190, 100.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein FUMARASE / YFUM


Mass: 53244.672 Da / Num. of mol.: 1 / Mutation: K289R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FUM1 / Plasmid: PASKYMFUM / Cellular location (production host): CYTOPLASM / Gene (production host): FUM1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P08417, fumarate hydratase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.3
Details: 150 MM TRIS-HCL PH 8.3, 100 MM LI2SO4, 8-10% PEG 4000
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1150 mMTris-HCl11
2100 mM11Li2SO4
38-10 %PEG400011

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→10 Å / Num. obs: 14127 / % possible obs: 94.5 % / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.109 / Rsym value: 0.154 / Net I/σ(I): 6.9
Reflection shellResolution: 2.59→2.62 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.487 / Rsym value: 0.54 / % possible all: 67
Reflection
*PLUS
Num. measured all: 118256
Reflection shell
*PLUS
% possible obs: 66.7 %

-
Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUO

1fuo


Resolution: 2.6→30 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.315 2558 10 %RANDOM
Rwork0.196 ---
obs0.196 14127 60 %-
Displacement parametersBiso mean: 24.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 0 0 3439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.94
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8 /
Num. reflection% reflection
Rwork57 -
obs-60 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11555
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.94
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.5

+
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