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- PDB-1cxr: AUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBI... -

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Basic information

Entry
Database: PDB / ID: 1cxr
TitleAUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBIN(S22/I25) WITH SELF-CORRECTING DISTANCE GEOMETRY BASED NOAH/DIAMOD PROGRAMS
ComponentsCRAMBIN
KeywordsPLANT PROTEIN / CRAMBIN / CRAMBE ABYSSINICA / PLANT SEED PROTEIN FEB. 20 / 1997
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 / SELF-CORRECTING DISTANCE GEOMETRY
AuthorsXu, Y. / Wu, J. / Gorenstein, D. / Braun, W.
Citation
Journal: J.Magn.Reson. / Year: 1999
Title: Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs.
Authors: Xu, Y. / Wu, J. / Gorenstein, D. / Braun, W.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Automated Assignment of Simulated, Experimental Noesy Spectra of Proteins by Feedback Filtering and Self-Correcting Distance Geometry
Authors: Mumenthaler, C. / Braun, W.
#2: Journal: J.Biomol.NMR / Year: 1997
Title: Automated Combined Assignment of Noesy Spectra and Three-Dimensional Protein Structure Determination
Authors: Mumenthaler, C. / Guntert, P. / Braun, W. / Wuthrich, K.
#3: Journal: Biological Magnetic Resonance / Year: 1999
Title: Combined Automated Assignment of NMR Spectra and Calculation of Three- Dimensional Protein Structures
Authors: Xu, Y. / Schein, C.H. / Braun, W.
#4: Journal: Biopolymers / Year: 1990
Title: A Program, Fantom, for Energy Refinement of Polypeptides and Proteins Using a Newton-Raphson Minimizer in the Torsion Angle Space
Authors: Schaumann, T.H. / Braun, W. / Wuthrich, K.
#5: Journal: J.Comput.Chem. / Year: 1998
Title: Exact and Efficient Analytical Calculation of the Accessible Surface Areas and Their Gradients Macromolecules
Authors: Fraczkiewicz, R. / Braun, W.
History
DepositionAug 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)4,7281
Polymers4,7281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION
RepresentativeModel #8closest to the average

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Components

#1: Protein/peptide CRAMBIN


Mass: 4728.410 Da / Num. of mol.: 1 / Fragment: ISOFORM OF CRAMBIN (46 RESIDUES) / Mutation: S22P, I25L / Source method: isolated from a natural source
Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Organ: SEED / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
222DQF-COSY
3332D TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 2.5 MM CRAMBIN(SER/ILE) 0.7 ML OF 75% D6-ACETONE, 20%H2O,5%D2O BUFFER
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian VXRS / Manufacturer: Varian / Model: VXRS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NOAH1C.MUMENTHALER, Y.XU, W.BRAUNstructure solution
DIAMOD1P. GUNTERT, W. BRAUN, K. WUTHRICHstructure solution
FANTOM4TH.SCHAUMANN, W.BRAUN, K.WUTHRICH, R.FRACZKIEWICZrefinement
RefinementMethod: SELF-CORRECTING DISTANCE GEOMETRY / Software ordinal: 1 / Details: SEE REFERENCE: J. MAGN. RESON. 136, P76-85(1999)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION
Conformers calculated total number: 40 / Conformers submitted total number: 10

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