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- PDB-2lw1: The C-terminal domain of the Uup protein is a DNA-binding coiled ... -

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Basic information

Entry
Database: PDB / ID: 2lw1
TitleThe C-terminal domain of the Uup protein is a DNA-binding coiled coil motif
ComponentsABC transporter ATP-binding protein uup
KeywordsDNA BINDING PROTEIN / ABC REG subfamily
Function / homology
Function and homology information


: / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to radiation / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
ABC transporter Uup, C-terminal / ATP-binding protein Uup / ABC transporter C-terminal domain / Valyl-tRNA synthetase, C-terminal domain / Valyl-tRNA synthetase, tRNA-binding arm superfamily / ABC-transporter extension domain / ABC transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter Uup, C-terminal / ATP-binding protein Uup / ABC transporter C-terminal domain / Valyl-tRNA synthetase, C-terminal domain / Valyl-tRNA synthetase, tRNA-binding arm superfamily / ABC-transporter extension domain / ABC transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Helix Hairpins / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP-binding protein Uup
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsCarlier, L. / Haase, A.S. / Burgos Zepeda, M.Y. / Dassa, E. / Lequin, O.
Citation
Journal: J.Struct.Biol. / Year: 2012
Title: The C-terminal domain of the Uup protein is a DNA-binding coiled coil motif.
Authors: Carlier, L. / Haase, A.S. / Burgos Zepeda, M.Y. / Dassa, E. / Lequin, O.
#1: Journal: Biomol.Nmr Assign. / Year: 2012
Title: Secondary structure and NMR resonance assignments of the C-terminal DNA-binding domain of Uup protein.
Authors: Carlier, L. / Haase, A.S. / Burgos Zepeda, M.Y. / Dassa, E. / Lequin, O.
History
DepositionJul 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Apr 27, 2016Group: Structure summary
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter ATP-binding protein uup


Theoretical massNumber of molelcules
Total (without water)12,1651
Polymers12,1651
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 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein ABC transporter ATP-binding protein uup


Mass: 12164.542 Da / Num. of mol.: 1 / Fragment: CTD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: uup, ycbH, ycbI, b0949, JW0932 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P43672

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N TOCSY
1322D 1H-15N HSQC
1423D HNCO
1523D HN(CA)CO
1623D CBCA(CO)NH
1723D HN(CA)CB
1823D HBHA(CO)NH
1933D (H)CCH-TOCSY
11023D C(CO)NH
11123D H(CCO)NH
11232D 1H-13C HSQC
11313D 1H-15N NOESY
11433D 1H-13C NOESY aliphatic
11533D 1H-13C NOESY aromatic
11612D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 15N] UUP, 170 mM sodium chloride, 30 mM TRIS, 0.111 mM DSS, 1 uM leupeptine, 1 uM pepstatine, 0.02 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-100% 13C; U-100% 15N] UUP, 170 mM sodium chloride, 30 mM TRIS, 0.111 mM DSS, 1 uM leupeptine, 1 uM pepstatine A, 0.02 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM [U-100% 13C; U-100% 15N] UUP, 170 mM sodium chloride, 30 mM TRIS, 1 uM leupeptine, 1 uM pepstatine A, 0.02 % sodium azide, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMUUP-1[U-100% 15N]1
170 mMsodium chloride-21
30 mMTRIS-31
0.111 mMDSS-41
1 uMleupeptine-51
1 uMpepstatine-61
0.02 %sodium azide-71
90 %H2O-81
10 %D2O-91
0.6 mMUUP-10[U-100% 13C; U-100% 15N]2
170 mMsodium chloride-112
30 mMTRIS-122
0.111 mMDSS-132
1 uMleupeptine-142
1 uMpepstatine A-152
0.02 %sodium azide-162
90 %H2O-172
10 %D2O-182
0.6 mMUUP-19[U-100% 13C; U-100% 15N]3
170 mMsodium chloride-203
30 mMTRIS-213
1 uMleupeptine-223
1 uMpepstatine A-233
0.02 %sodium azide-243
100 %D2O-253
Sample conditionsIonic strength: 200 / pH: 7.2 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIIBrukerAVANCE III5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardcollection
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpin2Bruker Biospingeometry optimization
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CHARMM22 force field
NMR constraintsNOE constraints total: 2176 / NOE intraresidue total count: 899 / NOE long range total count: 200 / NOE medium range total count: 365 / Hydrogen bond constraints total count: 14 / Protein chi angle constraints total count: 14 / Protein phi angle constraints total count: 72 / Protein psi angle constraints total count: 72
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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