[English] 日本語
Yorodumi
- PDB-2mat: E.COLI METHIONINE AMINOPEPTIDASE AT 1.9 ANGSTROM RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mat
TitleE.COLI METHIONINE AMINOPEPTIDASE AT 1.9 ANGSTROM RESOLUTION
ComponentsPROTEIN (METHIONINE AMINOPEPTIDASE)
KeywordsHYDROLASE / HYDROLASE(ALPHA-AMINOACYLPEPTIDE)
Function / homology
Function and homology information


: / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / ferrous iron binding / proteolysis / 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 / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLowther, W.T. / Orville, A.M. / Madden, D.T. / Lim, S. / Rich, D.H. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 1999
Title: Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis.
Authors: Lowther, W.T. / Orville, A.M. / Madden, D.T. / Lim, S. / Rich, D.H. / Matthews, B.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: The anti-angiogenic agent fumagillin covalently modifies a conserved active-site histidine in the Escherichia coli methionine aminopeptidase.
Authors: Lowther, W.T. / McMillen, D.A. / Orville, A.M. / Matthews, B.W.
#2: Journal: Biochemistry / Year: 1993
Title: Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli: a new type of proteolytic enzyme.
Authors: Roderick, S.L. / Matthews, B.W.
History
DepositionMar 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (METHIONINE AMINOPEPTIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5425
Polymers29,3421
Non-polymers2004
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.299, 67.683, 48.863
Angle α, β, γ (deg.)90.00, 111.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTEIN (METHIONINE AMINOPEPTIDASE)


Mass: 29341.775 Da / Num. of mol.: 1 / Mutation: R175Q
Source method: isolated from a genetically manipulated source
Details: SITE-DIRECTED MUTANT / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28B / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P07906, UniProt: P0AE18*PLUS, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLN 175, SITE-DIRECTED MUTANT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.1
Details: CRYSTALS OF THE CO(II)-SUBSTITUTED ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20-30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION IN STORAGE BUFFER(25 MM ...Details: CRYSTALS OF THE CO(II)-SUBSTITUTED ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20-30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION IN STORAGE BUFFER(25 MM HEPES PH 6.8, 25 MM K2SO4, 100 MM NACL, 1 MM COCL2, 15 MM METHIONINE),CONTAINING 48.8 MM N-OCTANOYL SUCROSE, 1:1 WITH WELL SOLUTIONS (24-26% PEG4000, 0.1M HEPES PH7.0-7.2,FRESH 2 MM COCL2)., pH 7.1, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: drop consists of 1:1 mixture of well and protein solutions
PH range low: 7.2 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
248.8 mMN-octanoyl sucrose1drop
324-26 %PEG40001reservoir
40.1 MHEPES1reservoir
52 mM1reservoirCoCl2

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 1998
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35.5 Å / Num. obs: 18444 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.077 / Net I/σ(I): 22.7
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 6.1 / Rsym value: 0.251 / % possible all: 100
Reflection
*PLUS
Num. measured all: 94123 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.251

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5F PRERELEASErefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MAT

1mat


Resolution: 1.9→35.5 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.155 18444 -
obs-18444 100 %
Solvent computationSolvent model: TNT / Bsol: 212.2 Å2 / ksol: 0.825 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 4 96 2091
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01220260.8
X-RAY DIFFRACTIONt_angle_deg2.327381.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.412240
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008512
X-RAY DIFFRACTIONt_gen_planes0.0132955
X-RAY DIFFRACTIONt_it4.120261
X-RAY DIFFRACTIONt_nbd0.0131810
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.013 / Weight: 5

+
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