[English] 日本語
Yorodumi
- PDB-4iec: Cys105 covalent modification by 2-hydroxyethyl disulfide in Mycob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iec
TitleCys105 covalent modification by 2-hydroxyethyl disulfide in Mycobacterium tuberculosis methionine aminopeptidase Type 1c
ComponentsMethionine aminopeptidase 2Methionyl aminopeptidase
KeywordsHYDROLASE / 2-hydroxyethyl disulfide / pita-bread fold / methionine aminopeptidase / cobalt
Function / homology
Function and homology information


: / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / cobalt ion binding / metalloaminopeptidase activity / protein processing / iron ion binding / metal ion binding / cytosol
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / : / Methionine aminopeptidase 2 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReddi, R. / Gumpena, R. / Kishor, C. / Addlagatta, A.
CitationJournal: Febs J. / Year: 2014
Title: Selective targeting of the conserved active site cysteine of Mycobacterium tuberculosis methionine aminopeptidase with electrophilic reagents
Authors: Reddi, R. / Arya, T. / Kishor, C. / Gumpena, R. / Ganji, R.J. / Bhukya, S. / Addlagatta, A.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Other
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionine aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0604
Polymers31,9031
Non-polymers1573
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.330, 48.241, 56.653
Angle α, β, γ (deg.)90.00, 95.17, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Methionine aminopeptidase 2 / Methionyl aminopeptidase / MAP / Peptidase M


Mass: 31903.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: map / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5J2, UniProt: P9WK19*PLUS, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2000 monomethyl ether, BisTris, Oxidized beta-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→38.82 Å / Num. all: 17628 / Num. obs: 16719 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.07 Å / % possible all: 97.7

-
Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.82 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.013 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.2 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23634 901 5.1 %RANDOM
Rwork0.16552 ---
all0.16906 17628 --
obs0.16906 16719 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.896 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 3 191 2355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222296
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.9533153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85423.93999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68715346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.131515
X-RAY DIFFRACTIONr_chiral_restr0.160.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211786
X-RAY DIFFRACTIONr_mcbond_it1.1771.51454
X-RAY DIFFRACTIONr_mcangle_it1.95522377
X-RAY DIFFRACTIONr_scbond_it3.0993842
X-RAY DIFFRACTIONr_scangle_it4.8294.5776
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 66 -
Rwork0.182 1234 -
obs--97.89 %

+
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