[English] 日本語
Yorodumi
- PDB-5d6b: Human fumarase (wild type) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d6b
TitleHuman fumarase (wild type)
ComponentsFumarate hydratase, mitochondrialFumarase
KeywordsLYASE / TCA cycle / fumarate hydratase
Function / homology
Function and homology information


regulation of arginine metabolic process / tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / Citric acid cycle (TCA cycle) / malate metabolic process / urea cycle / positive regulation of double-strand break repair via nonhomologous end joining / homeostasis of number of cells within a tissue ...regulation of arginine metabolic process / tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / Citric acid cycle (TCA cycle) / malate metabolic process / urea cycle / positive regulation of double-strand break repair via nonhomologous end joining / homeostasis of number of cells within a tissue / tricarboxylic acid cycle / site of double-strand break / chromosome / positive regulation of cold-induced thermogenesis / histone binding / mitochondrial matrix / DNA repair / DNA damage response / mitochondrion / extracellular exosome / nucleus / cytosol / cytoplasm
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 / Ribonucleotide Reductase Protein R1; domain 1 ...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 / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsPereira de Padua, R.A. / Nonato, M.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2008/08262-6 Brazil
Sao Paulo Research Foundation (FAPESP)2008/11644-8 Brazil
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of recombinant human fumarase.
Authors: Pereira de Padua, R.A. / Nonato, M.C.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fumarate hydratase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)49,7391
Polymers49,7391
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.420, 147.150, 57.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-794-

HOH

21A-808-

HOH

31A-827-

HOH

-
Components

#1: Protein Fumarate hydratase, mitochondrial / Fumarase / Fumarase


Mass: 49739.008 Da / Num. of mol.: 1 / Fragment: unp residues 49-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P07954, fumarate hydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM sodium malonate, 12% polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.1→31.67 Å / Num. obs: 27725 / % possible obs: 89.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 3.6

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementResolution: 2.1→31.67 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 1415 5.1 %
Rwork0.1796 26308 -
obs0.1827 27723 89.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.88 Å2 / Biso mean: 19.663 Å2 / Biso min: 6.25 Å2
Refinement stepCycle: final / Resolution: 2.1→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 0 250 3694
Biso mean---24.4 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083543
X-RAY DIFFRACTIONf_angle_d1.0674810
X-RAY DIFFRACTIONf_chiral_restr0.041560
X-RAY DIFFRACTIONf_plane_restr0.006627
X-RAY DIFFRACTIONf_dihedral_angle_d12.4411312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.17510.24951430.18992732287594
2.1751-2.26210.25241370.17582726286394
2.2621-2.36510.26061560.17232692284893
2.3651-2.48970.24781500.16282689283992
2.4897-2.64560.2421500.17242626277691
2.6456-2.84980.22411220.18352656277889
2.8498-3.13630.28721450.19882577272288
3.1363-3.58960.25461190.2022584270387
3.5896-4.52040.22971560.16882504266085
4.5204-31.67350.19391370.17192522265981

+
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