[English] 日本語
Yorodumi
- PDB-4s2r: Crystal structure of X-prolyl aminopeptidase from Caenorhabditis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4s2r
TitleCrystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site
ComponentsProtein APP-1
KeywordsHYDROLASE / pitta-bread fold / metalloprotease / Zinc binding
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / metalloaminopeptidase activity / proteolysis involved in protein catabolic process / protein homodimerization activity / proteolysis / zinc ion binding / cytoplasm
Similarity search - Function
Peptidase M24, C-terminal domain / Aminopeptidase P / C-terminal region of peptidase_M24 / Creatinase/Prolidase N-terminal domain / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase ...Peptidase M24, C-terminal domain / Aminopeptidase P / C-terminal region of peptidase_M24 / Creatinase/Prolidase N-terminal domain / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / 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 app-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsIyer, S. / La-Borde, P. / Payne, K.A.P. / Parsons, M.R. / Turner, A.J. / Isaac, R.E. / Acharya, K.R.
CitationJournal: FEBS Open Bio / Year: 2015
Title: Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site.
Authors: Iyer, S. / La-Borde, P.J. / Payne, K.A. / Parsons, M.R. / Turner, A.J. / Isaac, R.E. / Acharya, K.R.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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
P: Protein APP-1
Q: Protein APP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6896
Polymers144,4272
Non-polymers2624
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-174 kcal/mol
Surface area48180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.377, 87.910, 114.764
Angle α, β, γ (deg.)90.00, 115.92, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Protein APP-1


Mass: 72213.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: app-1, CELE_W03G9.4, W03G9.4 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon-Plus (DE3)-RIL / References: UniProt: O44750, Xaa-Pro aminopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 8.5, 17.5% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.93→38.872 Å / Num. all: 92214 / Num. obs: 91904 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.9
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 1.9 / % possible all: 82.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CTZ

3ctz


Resolution: 1.949→38.872 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 4454 5.01 %
Rwork0.1632 --
obs0.1658 88980 96.51 %
all-92251 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→38.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9735 0 4 596 10335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079998
X-RAY DIFFRACTIONf_angle_d1.02813563
X-RAY DIFFRACTIONf_dihedral_angle_d13.5213641
X-RAY DIFFRACTIONf_chiral_restr0.0411509
X-RAY DIFFRACTIONf_plane_restr0.0051729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.949-1.97150.32931230.24412260X-RAY DIFFRACTION77
1.9715-1.99470.28741270.21662758X-RAY DIFFRACTION94
1.9947-2.01910.25061340.20382738X-RAY DIFFRACTION96
2.0191-2.04460.27371330.19992840X-RAY DIFFRACTION96
2.0446-2.07150.281370.22817X-RAY DIFFRACTION97
2.0715-2.09990.26381430.1952820X-RAY DIFFRACTION97
2.0999-2.12990.28091480.18272825X-RAY DIFFRACTION97
2.1299-2.16170.25231310.18072828X-RAY DIFFRACTION97
2.1617-2.19550.24961610.17972915X-RAY DIFFRACTION98
2.1955-2.23140.2381470.18042819X-RAY DIFFRACTION98
2.2314-2.26990.26821600.18382800X-RAY DIFFRACTION98
2.2699-2.31120.23841550.17412842X-RAY DIFFRACTION97
2.3112-2.35560.22391580.17182807X-RAY DIFFRACTION97
2.3556-2.40370.26431390.17732820X-RAY DIFFRACTION97
2.4037-2.4560.23361530.18162781X-RAY DIFFRACTION95
2.456-2.51310.24831530.18382740X-RAY DIFFRACTION95
2.5131-2.57590.27961380.18552855X-RAY DIFFRACTION99
2.5759-2.64560.24851600.18452870X-RAY DIFFRACTION99
2.6456-2.72340.25391500.18832927X-RAY DIFFRACTION99
2.7234-2.81130.24221640.19132852X-RAY DIFFRACTION99
2.8113-2.91170.25091630.19022876X-RAY DIFFRACTION99
2.9117-3.02820.21731800.1932863X-RAY DIFFRACTION99
3.0282-3.1660.23841620.18772893X-RAY DIFFRACTION99
3.166-3.33280.23951520.17932896X-RAY DIFFRACTION98
3.3328-3.54150.22571390.15992755X-RAY DIFFRACTION95
3.5415-3.81480.17031390.14252846X-RAY DIFFRACTION96
3.8148-4.19820.14551550.1242920X-RAY DIFFRACTION100
4.1982-4.80480.16711500.11372915X-RAY DIFFRACTION99
4.8048-6.04980.16461670.12452883X-RAY DIFFRACTION98
6.0498-38.87950.1471330.13742765X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 54.6527 Å / Origin y: 63.0683 Å / Origin z: 25.4191 Å
111213212223313233
T0.1606 Å20.0399 Å20.0057 Å2-0.1834 Å20.0076 Å2--0.1484 Å2
L0.4787 °2-0.0162 °2-0.1078 °2-0.4447 °20.0491 °2--0.2841 °2
S-0.0029 Å °0.0625 Å °-0.0028 Å °-0.005 Å °0.029 Å °-0.0019 Å °-0.0389 Å °-0.0459 Å °-0.0253 Å °
Refinement TLS groupSelection details: ALL

+
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://pdbjlvh1.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