[English] 日本語
Yorodumi
- PDB-3g7k: Crystal Structure of Methylitaconate-delta-isomerase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g7k
TitleCrystal Structure of Methylitaconate-delta-isomerase
Components3-methylitaconate isomerase
KeywordsISOMERASE / DapF family fold / closed conformation / open conformation
Function / homology
Function and homology information


methylitaconate Delta-isomerase / methylitaconate delta-isomerase activity / nicotinate catabolic process
Similarity search - Function
PrpF protein / PrpF protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
3-methylitaconate isomerase
Similarity search - Component
Biological speciesEubacterium barkeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMesserschmidt, A. / Macieira, S. / Velarde, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from Eubacterium barkeri
Authors: Velarde, M. / Macieira, S. / Hilberg, M. / Broker, G. / Tu, S.-M. / Golding, B.T. / Pierik, A.J. / Buckel, W. / Messerschmidt, A.
History
DepositionFeb 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 28, 2025Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-methylitaconate isomerase
B: 3-methylitaconate isomerase
C: 3-methylitaconate isomerase
D: 3-methylitaconate isomerase


Theoretical massNumber of molelcules
Total (without water)166,2894
Polymers166,2894
Non-polymers00
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 3-methylitaconate isomerase
B: 3-methylitaconate isomerase


Theoretical massNumber of molelcules
Total (without water)83,1442
Polymers83,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-4 kcal/mol
Surface area29290 Å2
MethodPISA
3
C: 3-methylitaconate isomerase
D: 3-methylitaconate isomerase


Theoretical massNumber of molelcules
Total (without water)83,1442
Polymers83,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-2 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.078, 142.077, 228.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
3-methylitaconate isomerase / Methylitaconate-delta-isomerase


Mass: 41572.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium barkeri (bacteria) / Gene: Mii / Plasmid: pALD(EL)2-Kann(blue), pASG3_mii / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q0QLE6, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein solution: 150mM Tris/HCl, 150mM NaCl; Reservoir solution: 23% PEG 1500, 18% glycerol anhydrous. 0.001ml protein plus 0.001ml reservoir, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0707 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2008
Details: LN2 cooled fixed-exit, Si(111) monochromator; Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0707 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 47521 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 20.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.434 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PW0

2pw0


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.989 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 1.101 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25559 2402 5.1 %RANDOM
Rwork0.19986 ---
obs0.20267 45050 97.78 %-
all-63650 --
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: 46.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2--1.69 Å20 Å2
3----3.11 Å2
Refine analyzeLuzzati coordinate error free: 0.298 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10127 0 0 465 10592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.97313968
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49751364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32225.152396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.102151718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9711552
X-RAY DIFFRACTIONr_chiral_restr0.0950.21672
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027649
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.24756
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.26911
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2664
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7041.56961
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.182210989
X-RAY DIFFRACTIONr_scbond_it1.61933657
X-RAY DIFFRACTIONr_scangle_it2.6834.52979
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.703→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 170 -
Rwork0.252 3063 -
obs--91.66 %

+
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