[English] 日本語
Yorodumi
- PDB-3hfk: Crystal structure of 4-methylmuconolactone methylisomerase (H52A)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hfk
TitleCrystal structure of 4-methylmuconolactone methylisomerase (H52A) in complex with 4-methylmuconolactone
Components4-methylmuconolactone methylisomerase
KeywordsISOMERASE / ferredoxin / ferredoxin-like fold / beta-barrel / 4-methylmuconolactone methylisomerase / H52A / biodegradation / ortho-cleavage
Function / homology
Function and homology information


4-Methylmuconolactone methyl-isomerase / Methylmuconolactone methyl-isomerase / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4ML / 4-methylmuconolactone methylisomerase
Similarity search - Component
Biological speciesPseudomonas reinekei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMarin, M. / Heinz, D.W. / Pieper, D.H. / Klink, B.U.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure and catalytic mechanism of 4-methylmuconolactone methylisomerase
Authors: Marin, M. / Heinz, D.W. / Pieper, D.H. / Klink, B.U.
History
DepositionMay 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-methylmuconolactone methylisomerase
B: 4-methylmuconolactone methylisomerase
C: 4-methylmuconolactone methylisomerase
D: 4-methylmuconolactone methylisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39911
Polymers54,3064
Non-polymers1,0937
Water9,332518
1
A: 4-methylmuconolactone methylisomerase
D: 4-methylmuconolactone methylisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6225
Polymers27,1532
Non-polymers4683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-26 kcal/mol
Surface area10850 Å2
MethodPISA
2
B: 4-methylmuconolactone methylisomerase
C: 4-methylmuconolactone methylisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7786
Polymers27,1532
Non-polymers6254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-26 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.170, 84.360, 150.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
4-methylmuconolactone methylisomerase


Mass: 13576.619 Da / Num. of mol.: 4 / Mutation: H52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas reinekei (bacteria) / Strain: MT1 / Gene: mmlI / Plasmid: pASKIBAmmlI / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: C5MR76, EC: 5.4.99.14
#2: Chemical
ChemComp-4ML / [(2S)-2-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid / 4-methylmuconolactone


Mass: 156.136 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H8O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 292 K / Method: hanging drop / pH: 5
Details: 25% PEG 1500, 0.1M MMT, hanging drop, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionNumber: 298041 / Rmerge(I) obs: 0.113 / D res high: 1.9 Å / D res low: 75.24 Å / Num. obs: 41197 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1075.2432197.610.029
610110010010.037
46322510010.043
34611699.610.062
2.73391610010.099
2.42.7610310010.147
2.22.4592597.510.259
22.2874810010.327
1.9257439910.564
ReflectionResolution: 1.9→75.24 Å / Num. obs: 41197 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.23 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.71
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.15 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.5 / % possible all: 99

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefmac_5.5.0071refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HDS

3hds


Resolution: 1.9→40.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.38 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23131 2079 5 %RANDOM
Rwork0.18463 ---
obs0.18698 39116 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 77 518 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224094
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9715570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45323.269208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8811532
X-RAY DIFFRACTIONr_chiral_restr0.1130.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213204
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9691.52338
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68323813
X-RAY DIFFRACTIONr_scbond_it2.5831756
X-RAY DIFFRACTIONr_scangle_it4.0494.51737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 131 -
Rwork0.308 2760 -
obs--95.98 %

+
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