[English] 日本語
Yorodumi
- PDB-4a2y: STRUCTURE OF THE HUMAN EOSINOPHIL CATIONIC PROTEIN IN COMPLEX WIT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a2y
TitleSTRUCTURE OF THE HUMAN EOSINOPHIL CATIONIC PROTEIN IN COMPLEX WITH CITRATE ANIONS
ComponentsEOSINOPHIL CATIONIC PROTEIN
KeywordsHYDROLASE / OXIDOREDUCTASE / ANTIMICROBIAL / CYTOTOXIC
Function / homology
Function and homology information


induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / azurophil granule lumen ...induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / azurophil granule lumen / antibacterial humoral response / endonuclease activity / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / innate immune response / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Eosinophil cationic protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBoix, E. / Pulido, D. / Moussaoui, M. / Nogues, V. / Russi, S.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: The Sulfate-Binding Site Structure of the Human Eosinophil Cationic Protein as Revealed by a New Crystal Form.
Authors: Boix, E. / Pulido, D. / Moussaoui, M. / Nogues, V. / Russi, S.
History
DepositionSep 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EOSINOPHIL CATIONIC PROTEIN
B: EOSINOPHIL CATIONIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2778
Polymers31,1982
Non-polymers1,0796
Water5,585310
1
A: EOSINOPHIL CATIONIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1014
Polymers15,5991
Non-polymers5023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EOSINOPHIL CATIONIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1754
Polymers15,5991
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.511, 62.511, 174.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

-
Components

#1: Protein EOSINOPHIL CATIONIC PROTEIN / ECP / RIBONUCLEASE 3 / RNASE 3


Mass: 15598.876 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: EOSINOPHIL / Plasmid: PET11C/ECP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRECOMBINANT PROTEIN EXPRESSED USING A SYNTHETIC GENE (BOIX ET AL. J.BIOL.CHEM. 274, 15605) BASED ON ...RECOMBINANT PROTEIN EXPRESSED USING A SYNTHETIC GENE (BOIX ET AL. J.BIOL.CHEM. 274, 15605) BASED ON THE NP_002926 NATURAL VARIANT (THR97ARG)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 47.4 % / Description: NONE
Crystal growpH: 5.2
Details: 0.1 M NA CITRATE, PH 5.2, 6% JEFFAMINE M-600, 10 MM KH2PO4/K2HPO4, PH 7, 10 MM FECL3.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.7→62.5 Å / Num. obs: 36817 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DYT

1dyt


Resolution: 1.7→62.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.503 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21964 1944 5 %RANDOM
Rwork0.19141 ---
obs0.19283 36817 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.504 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→62.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 73 310 2541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0212306
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.281.9523156
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86122.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40215341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0331532
X-RAY DIFFRACTIONr_chiral_restr0.1620.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0221846
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1371.51353
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84622224
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4513953
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0624.5931
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 147 -
Rwork0.274 2605 -
obs--97.55 %

+
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