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- PDB-1dvw: NMR structure of 18 residue peptide from merp protein -

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Basic information

Entry
Database: PDB / ID: 1dvw
TitleNMR structure of 18 residue peptide from merp protein
Components18 RESIDUE PEPTIDE FROM MERP PROTEIN
KeywordsMETAL BINDING PROTEIN / TURN
Function / homology
Function and homology information


mercury ion transmembrane transporter activity / mercury ion binding / periplasmic space
Similarity search - Function
Mercuric transport protein periplasmic component / Mercuric transport protein periplasmic component/copper chaperone CopZ / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA
Similarity search - Domain/homology
: / Mercuric transport protein periplasmic component
Similarity search - Component
MethodSOLUTION NMR / hybrid distance geometry, simulated annealing
AuthorsVeglia, G. / Porcelli, F. / De Silva, T.M. / Prantner, A.M. / Opella, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: The Structure of the Metal-Binding Motif GMTCAAC Is Similar in an 18-Residue Linear Peptide and the Mercury Binding Protein MerP
Authors: Veglia, G. / Porcelli, F. / De Silva, T.M. / Prantner, A.M. / Opella, S.J.
History
DepositionJan 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_asym_id / _struct_conn.ptnr2_label_atom_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
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: 18 RESIDUE PEPTIDE FROM MERP PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0072
Polymers1,8061
Non-polymers2011
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
RepresentativeModel #10fewest violations

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Components

#1: Protein/peptide 18 RESIDUE PEPTIDE FROM MERP PROTEIN


Mass: 1806.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 18 residue synthetic peptide / References: UniProt: P04129
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.5 mM peptide; 20 mM Phosphate buffer pH=6.5; 1mM DTT.
Solvent system: 10% D20, 90% H2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.84Brungerstructure solution
X-PLOR3.84Brungerrefinement
RefinementMethod: hybrid distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 81 restraints, 77 are NOE-derived distance constraints, 4 dihedral angle restraints.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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