[English] 日本語
Yorodumi
- PDB-7c18: Crystal structure of FumaraseC from Mannheimia succiniciproducens... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c18
TitleCrystal structure of FumaraseC from Mannheimia succiniciproducens in complex with Fumarate
ComponentsFumarate hydratase class II
KeywordsLYASE / FumaraseC / Mannheimia succiniciproducens / succinate production / TCA cycle
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
FUMARIC ACID / Fumarate hydratase class II
Similarity search - Component
Biological speciesMannheimia succiniciproducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsKim, B. / Lee, S.H. / Kim, K.-J.
CitationJournal: To Be Published
Title: Structural studies reveal the molecular mechanism of isocitrate lyase from Chloroflexus aurantiacus
Authors: Kim, B. / Lee, S.H. / Kim, K.-J.
History
DepositionMay 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fumarate hydratase class II
B: Fumarate hydratase class II
C: Fumarate hydratase class II
D: Fumarate hydratase class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,6268
Polymers201,1614
Non-polymers4644
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size-exclusive chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33820 Å2
ΔGint-195 kcal/mol
Surface area51110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.089, 104.276, 125.333
Angle α, β, γ (deg.)90.000, 94.100, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Fumarate hydratase class II / Fumarase C / Aerobic fumarase / Iron-independent fumarase


Mass: 50290.328 Da / Num. of mol.: 4 / Mutation: S319C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mannheimia succiniciproducens (strain MBEL55E) (bacteria)
Strain: MBEL55E / Gene: fumC, MS0760 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q65UJ3, fumarate hydratase
#2: Chemical
ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3350, 0.2M Potassium fluoride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 83884 / % possible obs: 97.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.055 / Rrim(I) all: 0.134 / Χ2: 4.204 / Net I/σ(I): 11.1 / Num. measured all: 403604
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.80.27340920.8460.150.3131.85696.3
2.14-2.1840.2641870.8570.1390.2971.96697.3
2.18-2.223.90.24841050.8660.1320.2822.01997.1
2.22-2.263.90.23241380.9020.1230.2642.14496.9
2.26-2.314.10.22641180.9050.1180.2572.29996.8
2.31-2.374.20.21341960.9270.1090.2412.4297.4
2.37-2.424.10.21141280.9280.1090.2382.62997.1
2.42-2.494.10.241240.9380.1030.2262.58297.1
2.49-2.564.30.18841890.9460.0960.2122.6497.4
2.56-2.654.40.17641730.9520.0870.1973.09397.1
2.65-2.744.50.16341250.960.0810.1833.28597.8
2.74-2.854.60.15541820.9660.0750.1733.597.9
2.85-2.984.90.14242000.9740.0680.1583.88698
2.98-3.1450.13242420.9790.0610.1464.19498.6
3.14-3.335.30.12142190.9830.0550.1334.77698.7
3.33-3.595.60.11242370.9870.0490.1235.66698.7
3.59-3.956.10.10942750.9880.0460.1197.25699.4
3.95-4.526.30.10342900.9890.0420.1118.00999.4
4.52-5.76.30.09242930.9920.0380.15.99699.5
5.7-506.50.08243710.9920.0340.0895.40599.3

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFE

1yfe


Resolution: 2.12→32.57 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.758 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.222
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4190 5 %RANDOM
Rwork0.1846 ---
obs0.1874 79682 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.04 Å2 / Biso mean: 20.324 Å2 / Biso min: 10.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å2-0.73 Å2
2---0.99 Å2-0 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 2.12→32.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13978 0 32 302 14312
Biso mean--24.57 22.14 -
Num. residues----1848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01314266
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713396
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.63919350
X-RAY DIFFRACTIONr_angle_other_deg1.3621.57231158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1851844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.224.161644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.902152418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8031552
X-RAY DIFFRACTIONr_chiral_restr0.080.21969
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216032
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022700
LS refinement shellResolution: 2.12→2.17 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.296 261 -
Rwork0.242 5050 -
obs--82.91 %

+
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