[English] 日本語
Yorodumi
- PDB-2q93: E. coli methionine aminopeptidase Mn-form with inhibitor B21 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q93
TitleE. coli methionine aminopeptidase Mn-form with inhibitor B21
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / aminopeptidase / dinuclear / Mn(II)-form / enzyme-inhibitor complex / metalloenzyme
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / ferrous iron binding / proteolysis / 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
5-(2-METHOXYPHENYL)-2-FUROIC ACID / : / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYe, Q.-Z.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop flexibility in selective inhibition of bacterial enzymes.
Authors: Ma, Z.Q. / Xie, S.X. / Huang, Q.Q. / Nan, F.J. / Hurley, T.D. / Ye, Q.Z.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5915
Polymers29,2401
Non-polymers3514
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.107, 62.340, 52.441
Angle α, β, γ (deg.)90.000, 108.800, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Methionine aminopeptidase / MAP / Peptidase M


Mass: 29239.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: map / Plasmid: pGEMEX-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AE18, methionyl aminopeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-B21 / 5-(2-METHOXYPHENYL)-2-FUROIC ACID


Mass: 218.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-15% PEG 20000, 0.1 M MES (pH 6.5), vapor diffusion, hanging drop, temperature 291K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→19.94 Å / Num. obs: 29294 / % possible obs: 93.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.03 / Rsym value: 0.03 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.40.0994.71368340440.09988.7
1.69-1.793.40.0628.91343939110.06290.5
1.79-1.913.60.0479.71348737130.04791.4
1.91-2.073.90.03220.31368635200.03292.8
2.07-2.263.90.02922.71275732840.02993.7
2.26-2.533.90.0319.51161629920.0395.4
2.53-2.923.90.02919.91042126930.02996.1
2.92-3.583.80.02522889623180.02597.4
3.58-5.063.80.02326.2682818010.02398.3
5.06-19.943.60.02720.8363910180.02797.7

-
Phasing

Phasing MRRfactor: 0.386 / Cor.coef. Fo:Fc: 0.607
Highest resolutionLowest resolution
Rotation3 Å19.94 Å
Translation3 Å19.94 Å

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XNZ

1xnz


Resolution: 1.6→19.94 Å / FOM work R set: 0.811 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.251 2918 9.3 %
Rwork0.226 --
obs-29277 92.9 %
Solvent computationBsol: 28.632 Å2
Displacement parametersBiso mean: 12.064 Å2
Baniso -1Baniso -2Baniso -3
1-0.502 Å20 Å20.246 Å2
2---0.307 Å20 Å2
3----0.195 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 19 224 2287
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.32
X-RAY DIFFRACTIONc_mcbond_it1.0071.5
X-RAY DIFFRACTIONc_scbond_it1.8952
X-RAY DIFFRACTIONc_mcangle_it1.3722
X-RAY DIFFRACTIONc_scangle_it2.6492.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.6-1.610.529700.517443513
1.61-1.620.51550.411529584
1.62-1.630.405540.391501555
1.63-1.650.337510.34502553
1.65-1.660.319550.386481536
1.66-1.670.396450.357510555
1.67-1.680.376510.375515566
1.68-1.70.423580.331528586
1.7-1.710.329640.325485549
1.71-1.720.284420.287517559
1.72-1.740.365590.309496555
1.74-1.750.342650.298522587
1.75-1.770.278660.274504570
1.77-1.790.238540.264499553
1.79-1.80.345550.278511566
1.8-1.820.332530.277519572
1.82-1.840.301610.243519580
1.84-1.860.27530.237501554
1.86-1.880.364600.255534594
1.88-1.90.296580.204506564
1.9-1.920.234590.206504563
1.92-1.940.239610.204543604
1.94-1.960.269450.211523568
1.96-1.990.244460.2529575
1.99-2.020.196690.194514583
2.02-2.040.273800.215500580
2.04-2.070.257730.235529602
2.07-2.10.2540.2528582
2.1-2.140.24580.218527585
2.14-2.170.273470.221550597
2.17-2.210.265530.222522575
2.21-2.250.216550.22535590
2.25-2.290.205570.21548605
2.29-2.340.177480.189540588
2.34-2.390.241590.21547606
2.39-2.440.246590.215540599
2.44-2.510.29520.21551603
2.51-2.570.216570.22530587
2.57-2.650.236550.217554609
2.65-2.730.243610.216543604
2.73-2.830.281670.214542609
2.83-2.940.263710.215543614
2.94-3.080.207470.219556603
3.08-3.240.279680.23556624
3.24-3.440.258680.221543611
3.44-3.710.192530.193565618
3.71-4.080.193630.19562625
4.08-4.660.198670.173560627
4.66-5.850.196630.212576639
5.85-200.188740.213577651
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein_1.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5YE2.paramYE2.top

+
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