[English] 日本語
Yorodumi
- PDB-1gyt: E. coli Aminopeptidase A (PepA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gyt
TitleE. coli Aminopeptidase A (PepA)
ComponentsCYTOSOL AMINOPEPTIDASELeucyl aminopeptidase
KeywordsHYDROLASE / PEPTIDASE / DNA RECOMBINATION / AMINOPEPTIDASE
Function / homology
Function and homology information


plasmid recombination / bacterial leucyl aminopeptidase / leucyl aminopeptidase / transcription antitermination factor activity, DNA binding / plasmid maintenance / metalloexopeptidase activity / peptide catabolic process / aminopeptidase activity / manganese ion binding / DNA-templated transcription ...plasmid recombination / bacterial leucyl aminopeptidase / leucyl aminopeptidase / transcription antitermination factor activity, DNA binding / plasmid maintenance / metalloexopeptidase activity / peptide catabolic process / aminopeptidase activity / manganese ion binding / DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases ...Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Cytosol aminopeptidase / Cytosol aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsStraeter, N.
CitationJournal: Embo J. / Year: 1999
Title: X-Ray Structure of Aminopeptidase a from Escherichia Coli and a Model for the Nucleoprotein Complex in Xer Site-Specific Recombination
Authors: Straeter, N. / Sherratt, D.J. / Colloms, S.D.
History
DepositionApr 29, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Feb 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOSOL AMINOPEPTIDASE
B: CYTOSOL AMINOPEPTIDASE
C: CYTOSOL AMINOPEPTIDASE
D: CYTOSOL AMINOPEPTIDASE
E: CYTOSOL AMINOPEPTIDASE
F: CYTOSOL AMINOPEPTIDASE
G: CYTOSOL AMINOPEPTIDASE
H: CYTOSOL AMINOPEPTIDASE
I: CYTOSOL AMINOPEPTIDASE
J: CYTOSOL AMINOPEPTIDASE
K: CYTOSOL AMINOPEPTIDASE
L: CYTOSOL AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)661,78052
Polymers659,34812
Non-polymers2,43240
Water67,0883724
1
A: CYTOSOL AMINOPEPTIDASE
B: CYTOSOL AMINOPEPTIDASE
C: CYTOSOL AMINOPEPTIDASE
D: CYTOSOL AMINOPEPTIDASE
E: CYTOSOL AMINOPEPTIDASE
F: CYTOSOL AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,89026
Polymers329,6746
Non-polymers1,21620
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: CYTOSOL AMINOPEPTIDASE
H: CYTOSOL AMINOPEPTIDASE
I: CYTOSOL AMINOPEPTIDASE
J: CYTOSOL AMINOPEPTIDASE
K: CYTOSOL AMINOPEPTIDASE
L: CYTOSOL AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,89026
Polymers329,6746
Non-polymers1,21620
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)178.000, 178.000, 244.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
CYTOSOL AMINOPEPTIDASE / Leucyl aminopeptidase / LEUCINE AMINOPEPTIDASE / LAP / LEUCYL AMINOPEPTIDASE / AMINOPEPTIDASE A/I


Mass: 54945.676 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PCA9 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): DS957
References: UniProt: P11648, UniProt: P68767*PLUS, leucyl aminopeptidase
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3724 / 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: 3.39 Å3/Da / Density % sol: 57.6 %
Crystal growpH: 8 / Details: 20 MM KCL, 50 MM TRIS PH 8.0, 1 MM MG(AC)2
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein11
2200 mM12KCl
350 mMTris12pH8.0
41 mM12Mg(OAc)2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.23
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 298951 / % possible obs: 99.9 % / Redundancy: 3 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 1198951 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
Highest resolution: 2.5 Å

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.002 / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME RESIDUES HAVE VERY WEAK DENSITY. THEY HAVE BEEN INCLUDED IN THE MODEL TO FACILITATE MODEL BUILDING STUDIES. CHECK THE DENSITY AND B-VALUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 14839 5 %RANDOM
Rwork0.165 ---
obs0.165 298907 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.7 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å24.12 Å20 Å2
2--2.22 Å20 Å2
3----4.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46152 0 76 3724 49952
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 2447 4.9 %
Rwork0.202 47216 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 500 Å / Num. reflection all: 298907 / Rfactor obs: 0.183 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
LS refinement shell
*PLUS
Rfactor obs: 0.202

+
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