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- PDB-2rrk: Solution structure of the E. coli ORF135 protein -

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Basic information

Entry
Database: PDB / ID: 2rrk
TitleSolution structure of the E. coli ORF135 protein
ComponentsCTP pyrophosphohydrolase
KeywordsHYDROLASE / pyrophospho hydrolase
Function / homology
Function and homology information


(d)CTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / hydrolase activity / DNA repair
Similarity search - Function
NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CTP pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKawasaki, K. / Mishima, M.
CitationJournal: To be Published
Title: Solution structure of the E. coli ORF135 protein
Authors: Kawasaki, K. / Mishima, M.
History
DepositionJan 1, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTP pyrophosphohydrolase


Theoretical massNumber of molelcules
Total (without water)15,4771
Polymers15,4771
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 / 100structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CTP pyrophosphohydrolase / ORF135


Mass: 15476.538 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P77788, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D HN(COCA)CB
1423D HN(CA)CO
1523D HNCO
1633D (H)CCH-TOCSY
1723D H(CCO)NH
1823D C(CO)NH
1924D HC(CO)NH
11033D 1H-13C NOESY aliphatic
11113D 1H-15N NOESY
11212D 15N filtered NOESY
11313D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-99% 15N] entity-1; 50mM potassium phosphate-2; 20mM potassium chloride-3; 1mM DTT-4; 0.1mM EDTA-5; 93% H2O/7% D2O93% H2O/7% D2O
21mM [U-99% 13C; U-99% 15N] entity-6; 50mM potassium phosphate-7; 20mM potassium chloride-8; 1mM DTT-9; 0.1mM EDTA-10; 93% H2O/7% D2O93% H2O/7% D2O
31mM [U-99% 13C; U-99% 15N] entity-11; 50mM potassium phosphate-12; 20mM potassium chloride-13; 1mM DTT-14; 0.1mM EDTA-15; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-99% 15N]1
50 mMpotassium phosphate-21
20 mMpotassium chloride-31
1 mMDTT-41
0.1 mMEDTA-51
1 mMentity-6[U-99% 13C; U-99% 15N]2
50 mMpotassium phosphate-72
20 mMpotassium chloride-82
1 mMDTT-92
0.1 mMEDTA-102
1 mMentity-11[U-99% 13C; U-99% 15N]3
50 mMpotassium phosphate-123
20 mMpotassium chloride-133
1 mMDTT-143
0.1 mMEDTA-153
Sample conditionsIonic strength: 70 / pH: 6.9 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardpeak picking
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3434 / NOE intraresidue total count: 603 / NOE long range total count: 1292 / NOE medium range total count: 574 / NOE sequential total count: 965 / Hydrogen bond constraints total count: 70 / Protein other angle constraints total count: 186 / Protein phi angle constraints total count: 93 / Protein psi angle constraints total count: 93
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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