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- PDB-1cxx: MUTANT R122A OF QUAIL CYSTEINE AND GLYCINE-RICH PROTEIN, NMR, MIN... -

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Basic information

Entry
Database: PDB / ID: 1cxx
TitleMUTANT R122A OF QUAIL CYSTEINE AND GLYCINE-RICH PROTEIN, NMR, MINIMIZED STRUCTURE
ComponentsCYSTEINE AND GLYCINE-RICH PROTEIN CRP2
KeywordsSIGNALING 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, MOLECULAR DYNAMICS REFINEMENT, ENERGY MINIMIZATION
AuthorsKloiber, K. / Weiskirchen, R. / Kraeutler, B. / Bister, K. / Konrat, R.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Mutational analysis and NMR spectroscopy of quail cysteine and glycine-rich protein CRP2 reveal an intrinsic segmental flexibility of LIM domains.
Authors: Kloiber, K. / Weiskirchen, R. / Krautler, B. / Bister, K. / Konrat, R.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_nmr_software.name / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYSTEINE AND GLYCINE-RICH PROTEIN CRP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1703
Polymers12,0401
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 11STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein CYSTEINE AND GLYCINE-RICH PROTEIN CRP2


Mass: 12039.655 Da / Num. of mol.: 1 / Fragment: CARBOXYL-TERMINAL LIM-DOMAIN / Mutation: R122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coturnix japonica (Japanese quail) / Cell: FIBROBLAST / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: Q05158
#2: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-SEPARATED NOESY
1313D-15N-SEPARATED TOCSY
141HNHA
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 15N-EDITED SPECTRA AND HOMONUCLEAR 2D SPECTRA

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Sample preparation

DetailsContents: 1.1MM QCRP2(LIM2)R122A 15N; 20MM POTASSIUM PHOSPHATE; 50MM POTASSIUM CHLORIDE; 0.5MM DTT;
Sample conditionspH: 7.0 / Pressure: AMBIENT / Temperature: 299 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ANSIG3.3KRAULIS, P. J.data analysis
X-PLOR3.1BRUNGERstructure solution
X-PLOR3.1BRUNGERrefinement
NMRPipe1.7DELAGLIO, F., GRZESISEK, S., VUISTER, G., ZHU, G. PFEIFER, J., BAX, A.processing
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS REFINEMENT, ENERGY MINIMIZATION
Software ordinal: 1
Details: THE STRUCTURE IS BASED ON 340 NOE-DERIVED DISTANCE RESTRAINTS AS WELL AS 16 DISTANCE RESTRAINTS DERIVED FROM HYDROGEN BONDS
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 11 / Conformers submitted total number: 1

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