[English] 日本語
Yorodumi
- PDB-1wl9: Structure of aminopeptidase P from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wl9
TitleStructure of aminopeptidase P from E. coli
ComponentsXaa-Pro aminopeptidase
KeywordsHYDROLASE / Proline-specific peptidase / metalloenzyme / pita-bread fold
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / : / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / : / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsGraham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2005
Title: Structural and functional implications of metal ion selection in aminopeptidase p, a metalloprotease with a dinuclear metal center
Authors: Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.
History
DepositionJun 22, 2004Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 16, 2005ID: 1AZ9
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn ...pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _struct_conn_type.id / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9054
Polymers49,7601
Non-polymers1453
Water10,935607
1
A: Xaa-Pro aminopeptidase
hetero molecules

A: Xaa-Pro aminopeptidase
hetero molecules

A: Xaa-Pro aminopeptidase
hetero molecules

A: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,62216
Polymers199,0404
Non-polymers58112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Unit cell
Length a, b, c (Å)177.420, 177.420, 96.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-1539-

HOH

DetailsThe biological assembly is a homotetramer generated by the symmetry operatiors: (x,y,z), (1-x,1-y,z), (y,x,4/3-z), (1-y,1-x,4/3-z)

-
Components

#1: Protein Xaa-Pro aminopeptidase / Aminopeptidase P / X-Pro aminopeptidase / Aminopeptidase P II / APP-II / Aminoacylproline aminopeptidase


Mass: 49760.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PEPP / Plasmid: pPL670 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: Tris, PEG 4k, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 3, 1997 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 65584 / % possible obs: 93 % / Observed criterion σ(I): -3 / Net I/σ(I): 24.4
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 5.69 / % possible all: 63.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Published hexagonal structure without Mn or solvent atoms

Resolution: 1.9→38.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.376 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17047 1991 3 %RANDOM
Rwork0.15185 ---
all0.15243 ---
obs0.15243 63537 93.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 3 607 4110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223585
X-RAY DIFFRACTIONr_bond_other_d0.0010.023253
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9564855
X-RAY DIFFRACTIONr_angle_other_deg0.82937539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87723.71186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87615612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0351533
X-RAY DIFFRACTIONr_chiral_restr0.0770.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
X-RAY DIFFRACTIONr_nbd_refined0.2050.2746
X-RAY DIFFRACTIONr_nbd_other0.1820.23383
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21755
X-RAY DIFFRACTIONr_nbtor_other0.0820.22148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.48122842
X-RAY DIFFRACTIONr_mcbond_other0.5952898
X-RAY DIFFRACTIONr_mcangle_it2.81533523
X-RAY DIFFRACTIONr_scbond_it2.63521601
X-RAY DIFFRACTIONr_scangle_it4.00631332
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
Rfree0.267 104 -
Rwork0.235 3053 -
obs--61.6 %
Refinement TLS params.Method: refined / Origin x: 64.821 Å / Origin y: 58.322 Å / Origin z: 49.737 Å
111213212223313233
T0.0065 Å20.0189 Å20.0055 Å2-0.0293 Å20.0008 Å2--0.0268 Å2
L0.1686 °2-0.1389 °20.0612 °2-0.3119 °2-0.0808 °2--0.3886 °2
S-0.0193 Å °0.0402 Å °0.0087 Å °0.0152 Å °-0.0274 Å °0.0214 Å °0.0533 Å °0.0114 Å °0.0467 Å °

+
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