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- PDB-1cwz: Solution structure of the analogue retro-inverso (MA-S)REGRIGGC i... -

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Basic information

Entry
Database: PDB / ID: 1cwz
TitleSolution structure of the analogue retro-inverso (MA-S)REGRIGGC in contact with the monoclonal antibody MAB 4X11, NMR, 7 structures
ComponentsHISTONE H3
KeywordsDNA BINDING PROTEIN / PSEUDOMIMETIC / SYNTHETIC PEPTIDE / RETRO-INVERSO ANALOGUE / TR-NOE / ANTIGEN- ANTIBODY COMPLEX
Function / homologyMETHYLMALONIC ACID
Function and homology information
MethodSOLUTION NMR / ENERGY MINIMISATION MOLECULAR DYNAMICS (SIMULATED ANNEALING)
AuthorsPhan Chan Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, M.T.
CitationJournal: Biochemistry / Year: 2001
Title: Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear Overhauser effect spectroscopy and molecular dynamics approach.
Authors: Phan-Chan-Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, M.T.
History
DepositionAug 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / 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_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9652
Polymers8471
Non-polymers1181
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 50structures with the lowest energy
RepresentativeModel #6lowest energy

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Components

#1: Protein/peptide HISTONE H3 /


Mass: 846.980 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN: Residues 130-135 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE CGG WAS ADDED AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE EXPERIMENTS VIA THE CYS THIOL GROUP. NH2-CO WAS ADDED AT THE C-TERMINAL ...Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE CGG WAS ADDED AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE EXPERIMENTS VIA THE CYS THIOL GROUP. NH2-CO WAS ADDED AT THE C-TERMINAL EXTREMITY OF THE RETRO-INVERSO PEPTIDE IN ORDER TO MIMIC THE N-TERMINAL OF THE PARENT PEPTIDE. ALL NON GLYCINE RESIDUE PRESENT A D-CONFIGURATION EXCEPT CYS. TWO RI(MA) DIASTEREISOMERS WERE OBTAINED AND COULDN'T BE SEPARATED.
#2: Chemical ChemComp-DXX / METHYLMALONIC ACID / Methylmalonic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: COSY, TOCSY, NOESY
NMR detailsText: THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1(I.E. 5 MM OF PEPTIDE AND 0.1 MM OF MAB)

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Sample preparation

DetailsContents: 5MM PEPTIDE, 0.1 MM MAB. 100 MM PHOSPHATE BUFFER CONTAINING 0.02% SODIUM AZIDE
Sample conditionsIonic strength: 0.1M PHOSPHATE / pH: 7 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.4GUNTERT, WUTHRICHstructure solution
Discover3MOLECULAR SIMULATIONS INC.structure solution
Discover3MOLECULAR SIMULATIONS INC.refinement
RefinementMethod: ENERGY MINIMISATION MOLECULAR DYNAMICS (SIMULATED ANNEALING)
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A SET OF 35 TO 60 BACKBONE-BACKBONE, BACKBONE-SIDE CHAIN AND SIDE CHAIN-SIDE CHAIN DISTANCE RESTRAINTS. THE PHI ANGLE FOR THE NON GLYCINE D-RESIDUES WAS ...Details: THE STRUCTURES ARE BASED ON A SET OF 35 TO 60 BACKBONE-BACKBONE, BACKBONE-SIDE CHAIN AND SIDE CHAIN-SIDE CHAIN DISTANCE RESTRAINTS. THE PHI ANGLE FOR THE NON GLYCINE D-RESIDUES WAS CONSTRAINED BETWEEN 0 AND 175. A DISTANCE DEPENDENT DIELECTRIC CONSTANT EQUAL TO 4R WAS APPLIED. THE NET ELECTRIC CHARGES WERE DECREASED, WHILE THOSE OF THE N AND C-TERMINAL CHARGED GROUPS WERE NEGLECTED.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 7

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