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- PDB-1zdb: PHAGE-SELECTED MINI PROTEIN A DOMAIN, Z38, NMR, MINIMIZED MEAN ST... -

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Entry
Database: PDB / ID: 1zdb
TitlePHAGE-SELECTED MINI PROTEIN A DOMAIN, Z38, NMR, MINIMIZED MEAN STRUCTURE
ComponentsMINI PROTEIN A DOMAIN, Z38
KeywordsIGG BINDING DOMAIN / PROTEIN A MIMIC
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / METRIX MATRIX DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS
AuthorsStarovasnik, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Structural mimicry of a native protein by a minimized binding domain.
Authors: Starovasnik, M.A. / Braisted, A.C. / Wells, J.A.
History
DepositionJul 9, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MINI PROTEIN A DOMAIN, Z38


Theoretical massNumber of molelcules
Total (without water)4,5691
Polymers4,5691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 56LOWEST RESTRAINT VIOLATION ENERGY
Representative

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Components

#1: Protein/peptide MINI PROTEIN A DOMAIN, Z38


Mass: 4569.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MINIMIZED, TWO-HELIX, IGG-BINDING VARIANT OF PROTEIN A
Source: (gene. exp.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111IN H2O: NOESY
121TOCSY
131COSY; IN D2O: NOESY
141COSY-35
1512Q

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Sample preparation

Sample conditionspH: 5.1 / Temperature: 281 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
DGIIHAVELrefinement
DGIIstructure solution
Discoverstructure solution
RefinementMethod: METRIX MATRIX DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST RESTRAINT VIOLATION ENERGY
Conformers calculated total number: 56 / Conformers submitted total number: 1

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