[English] 日本語
Yorodumi
- PDB-1ibi: QUAIL CYSTEINE AND GLYCINE-RICH PROTEIN, NMR, 15 MINIMIZED MODEL ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ibi
TitleQUAIL CYSTEINE AND GLYCINE-RICH PROTEIN, NMR, 15 MINIMIZED MODEL STRUCTURES
ComponentsCYSTEINE-RICH PROTEIN 2
KeywordsMETAL BINDING PROTEIN / LIM DOMAIN CONTAINING PROTEINS / METAL-BINDING PROTEIN
Function / homology
Function and homology information


cell differentiation / zinc ion binding / nucleus
Similarity search - Function
Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
Cysteine and glycine-rich protein 2
Similarity search - Component
Biological speciesCoturnix japonica (Japanese quail)
MethodSOLUTION NMR / simulated annealing
AuthorsSchuler, W. / Kloiber, K. / Matt, T. / Bister, K. / Konrat, R.
Citation
Journal: Biochemistry / Year: 2001
Title: Application of cross-correlated NMR spin relaxation to the zinc-finger protein CRP2(LIM2): evidence for collective motions in LIM domains.
Authors: Schuler, W. / Kloiber, K. / Matt, T. / Bister, K. / Konrat, R.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: STRUCTURE OF CYSTEINE- AND GLYCINE-RICH PROTEIN CRP2
Authors: Konrat, R. / Kraeutler, B. / Weiskirchen, R. / Bister, K.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Solution Structure of the Carboxyl-terminal LIM Domain from Quail Cystein-rich Protein CRP2
Authors: Konrat, R. / Weiskirchen, R. / Kraeutler, B. / Bister, K.
History
DepositionMar 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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: CYSTEINE-RICH PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2573
Polymers12,1261
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein CYSTEINE-RICH PROTEIN 2 / CRP2


Mass: 12125.771 Da / Num. of mol.: 1 / Fragment: C-TERMINAL LIM DOMAIN, RESIDUES 82-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coturnix japonica (Japanese quail) / Gene: CSRP2 / Plasmid: PET3D-QCRP2(LIM2) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q05158
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC
1213D HNCA
1313D HN(CA)CB
1413D HNCO
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1713D CCH-TOCSY-NNH
1813D 13C-NOESY-HSQC (CA-centered)
1913D 13C-NOESY-HSQC (methyl-centered)
11023D 15N-NOESY-HSQC
NMR detailsText: Projection data related to the backbone dihedrals phi, psi from CaHa(i)-DD/C'(i)-CSA and CAHA(i)-DD/C'(i-1)-CSA relaxation and 15N(i)-1HN(i)-DD/13CO(i)-CSA and 1H(i)-15N(i)-13C'(i) DD-CSA cross ...Text: Projection data related to the backbone dihedrals phi, psi from CaHa(i)-DD/C'(i)-CSA and CAHA(i)-DD/C'(i-1)-CSA relaxation and 15N(i)-1HN(i)-DD/13CO(i)-CSA and 1H(i)-15N(i)-13C'(i) DD-CSA cross correlation experiments. Side-chain dihedral angles chi1 from 2D quantitative J-spectroscopy experiments giving access to 3J(CO,Cgamma) and 3J(N,Cgamma). Differential relaxation of multiple-quantum coherences Gamma(i,j)=R(DQ)-R(ZQ), i,j denote 15N,1HN or 13C',15N, respectively.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11-2mM qCRP2(LIM2) U-15N,13C; 20 mM potassium phosphate, 50mM KCl, 0.5mM dithiothreitol, 90% H2O, 10% D2O90% H2O/10% D2O
21-2mM qCRP2(LIM2) U-15N; 20 mM potassium phosphate, 50mM KCl, 0.5mM dithiothreitol, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 20mM potassium phosphate; 50mM KCl / pH: 7.2 / Pressure: ambient / Temperature: 299 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS 500 / Manufacturer: Varian / Model: UNITYPLUS 500 / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMRv6.1 Rev.BVarian Associates, Inc.collection
NMRPipev1.8 Rev 2001.030.21.27Delaglio, F.processing
ANSIGv3.3Kraulis, P.data analysis
CNS1Brunger, A.structure solution
X-PLOR3.851Brunger, A.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: This entry represents the C-terminal LIM domain of the quail cysteine rich protein CRP2(LIM2) consisting of 15 minimized final structures. Residues MET 82 - ALA 117 and ASN 175 - GLN 194 ...Details: This entry represents the C-terminal LIM domain of the quail cysteine rich protein CRP2(LIM2) consisting of 15 minimized final structures. Residues MET 82 - ALA 117 and ASN 175 - GLN 194 were not observed and there is no information regarding the conformation that these residues may adopt in solution. The only stretch of residues for which there is structural information is GLU 118 - LYS 174 so the simulations were restricted to the central part ALA 117 - ASN 175, containing the two zinc knuckles. In an initial stage zinc was covalently attached to a linearized template structure, then tetrahedral coordination was enforced by distance constraints. Finally the zinc ions were covalently attached to the coordinating residues using standard force field parameters. 653 inter- and intra-residue NOE restraints were defined as strong, medium, weak and very weak and applied during the final refinement as well as 28 torsion angle restraints and 15 hydrogen bond restraints. Omega dihedral angles were restrained to trans (E). Average rmsd from exp. distance restraints(angstroms) 0.01, average rmsd from idealized covalent geometry: bonds(angstroms): 0.01; angles(deg) 1.98;
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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