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- PDB-1ghh: SOLUTION STRUCTURE OF DINI -

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Basic information

Entry
Database: PDB / ID: 1ghh
TitleSOLUTION STRUCTURE OF DINI
ComponentsDNA-DAMAGE-INDUCIBLE PROTEIN I
KeywordsPROTEIN BINDING / bicelle / DinI / dipolar coupling / liquid crystal / Pf1 / RecA
Function / homology
Function and homology information


SOS response / DNA repair / enzyme binding
Similarity search - Function
DinI-like / DNA damage-inducible protein DinI-like / DinI-like superfamily / DinI-like family / Protein Binding, DinI Protein; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA damage-inducible protein I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, molecular dynamics in Cartesian space
AuthorsRamirez, B.E. / Voloshin, O.N. / Camerini-Otero, R.D. / Bax, A.
CitationJournal: Protein Sci. / Year: 2000
Title: Solution structure of DinI provides insight into its mode of RecA inactivation.
Authors: Ramirez, B.E. / Voloshin, O.N. / Camerini-Otero, R.D. / Bax, A.
History
DepositionDec 19, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionJan 10, 2001ID: 1F0A
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: 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: DNA-DAMAGE-INDUCIBLE PROTEIN I


Theoretical massNumber of molelcules
Total (without water)8,9581
Polymers8,9581
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)20 / 30structures with the lowest energy
Representative

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Components

#1: Protein DNA-DAMAGE-INDUCIBLE PROTEIN I / DINI


Mass: 8957.937 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABR1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1322D NOESY
141HNCG
151HN(CO)CG
263IPAP 15N HSQC
273HNCO
283(HA)CA(CO)NH
NMR detailsText: This structure was determined using two sets of dipolar coupling restraints. One set was recorded in a bicelle liquid crystal solution; the other set was recorded in a phage liquid crystal ...Text: This structure was determined using two sets of dipolar coupling restraints. One set was recorded in a bicelle liquid crystal solution; the other set was recorded in a phage liquid crystal solution. See citation 1 for details on solution conditions. A total of 127 N-H, 135 CA-HA, 138 CA-CO, 61 N-CO, and 64 CO-HN dipolar restraints were used in the structure calculation. Additional restraints included 592 intraresidue, 278 short range, 104 medium range, and 140 long range NOE restraints as well as 76 phi, 51 psi, and 21 chi1 dihedral restraints. A conformational database was employed in the simulated annealing calculation. No radius of gyration term was employed in the simulated annealing calculation.

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Sample preparation

Details
Solution-IDContents
10.6 mM DinI U-13C,15N, 20 mM phosphate buffer, 100 mM NaCl; pH 6.6; 95% H2O, 5% D2O
20.6 mM DinI U-13C,15N, 20 mM phosphate buffer, 100 mM NaCl; pH 6.6; 99% D2O, 1% H2O
30.6 mM DinI U-13C,15N, 20 mM phosphate buffer, 100 mM NaCl; pH 6.6; BICELLE OR PHAGE LIQUID CRYSTAL, 95% H2O, 5% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.6AMBIENT 298.0 K
26.6AMBIENT 298.0 K
36.6AMBIENT 302.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglioprocessing
PIPPGarrettdata analysis
X-PLORBrungerrefinement
X-PLORBrungerstructure solution
RefinementMethod: simulated annealing, molecular dynamics in Cartesian space
Software ordinal: 1
Details: Structures were calculated in a three stage process. In the first stage, folds were calculated from a fully-extended chain based only on torsion and NOE restraints. In the second stage, the ...Details: Structures were calculated in a three stage process. In the first stage, folds were calculated from a fully-extended chain based only on torsion and NOE restraints. In the second stage, the ten best structures of stage 1 were used as starting structures in a simulated annealing calculation that included dipolar restraints measured in bicelles. In the last stage, the ten lowest energy structures of Stage 2 were used as starting structures in a simulated annealing calculation that also included dipolar restraints measured in a phage liquid crystal.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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