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- PDB-1ccm: DIRECT NOE REFINEMENT OF CRAMBIN FROM 2D NMR DATA USING A SLOW-CO... -

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Basic information

Entry
Database: PDB / ID: 1ccm
TitleDIRECT NOE REFINEMENT OF CRAMBIN FROM 2D NMR DATA USING A SLOW-COOLING ANNEALING PROTOCOL
ComponentsCRAMBIN
KeywordsPLANT SEED PROTEIN
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCrambe hispanica subsp. abyssinica (Abyssinian crambe)
MethodSOLUTION NMR
AuthorsBonvin, A.M.J.J. / Rullmann, J.A.C. / Lamerichs, R.M.J.N. / Boelens, R. / Kaptein, R.
Citation
Journal: Proteins / Year: 1993
Title: "Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
Authors: Bonvin, A.M. / Rullmann, J.A. / Lamerichs, R.M. / Boelens, R. / Kaptein, R.
#1: Journal: Proteins / Year: 1993
Title: "Ensemble" Iterative Relaxation Matrix Approach: A New NMR Refinement Protocol Applied to the Solution Structure of Crambin
Authors: Bonvin, A.M.J.J. / Rullmann, J.A.C. / Lamerichs, R.M.J.N. / Boelens, R. / Kaptein, R.
#2: Journal: COMPUTATION OF BIOMOLECULAR STRUCTURES; ACHIEVEMENTS PROBLEMS, AND PERSPECTIVES
Year: 1992
Title: Structure Determination by NMR-Application to Crambin
Authors: Rullmann, J.A.C. / Bonvin, A.M.J.J. / Boelens, R. / Kaptein, R.
#3: Journal: Thesis / Year: 1989
Title: 2D NMR Studies of Biomolecules: Protein Structure and Protein-DNA Interactions
Authors: Lamerichs, R.M.J.M.
#4: Journal: Eur.J.Biochem. / Year: 1988
Title: Secondary Structure and Hydrogen Bonding of Crambin in Solution
Authors: Lamerichs, R.M.J.N. / Berliner, L.J. / Boelens, R. / Demarco, A. / Llinas, M. / Kaptein, R.
#5: Journal: FEBS Lett. / Year: 1987
Title: 1H NMR Characterization of Two Crambin Species
Authors: Vermeulen, J.A.W.H. / Lamerichs, R.M.J.M. / Berliner, L.J. / Demarco, A. / Llinas, M. / Boelens, R. / Alleman, J. / Kaptein, R.
History
DepositionApr 14, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRAMBIN


Theoretical massNumber of molelcules
Total (without water)4,7381
Polymers4,7381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: ARG 17 - LEU 18 OMEGA ANGLE = 147.581 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION IN MODEL 7
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / -
Representative

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Components

#1: Protein/peptide CRAMBIN


Mass: 4738.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: GROMOS / Developer: VAN GUNSTEREN,BERENDSEN / Classification: refinement
NMR ensembleConformers submitted total number: 8

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