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- PDB-2mpj: NMR structure of Xenopus RecQ4 zinc knuckle -

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Basic information

Entry
Database: PDB / ID: 2mpj
TitleNMR structure of Xenopus RecQ4 zinc knuckle
ComponentsRECQL4-helicase-like protein
KeywordsNUCLEOTIDE BINDING PROTEIN / zinc knuckle / RecQ4 / helicase / DNA/RNA binding / protein
Function / homology
Function and homology information


DNA 3'-5' helicase / DNA replication initiation / helicase activity / DNA replication / nucleic acid binding / chromatin binding / chromatin / zinc ion binding / ATP binding / nucleus
Similarity search - Function
DNA replication/checkpoint protein / DNA replication and checkpoint protein / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. ...DNA replication/checkpoint protein / DNA replication and checkpoint protein / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA 3'-5' helicase / DNA 3'-5' helicase
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsZucchelli, C. / Marino, F. / Mojumdar, A. / Onesti, S. / Musco, G.
CitationJournal: Sci Rep / Year: 2016
Title: Structural and biochemical characterization of an RNA/DNA binding motif in the N-terminal domain of RecQ4 helicases
Authors: Marino, F. / Mojumdar, A. / Zucchelli, C. / Bhardwaj, A. / Buratti, E. / Vindigni, A. / Musco, G. / Onesti, S.
History
DepositionMay 23, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: 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_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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: RECQL4-helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6792
Polymers2,6141
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide RECQL4-helicase-like protein


Mass: 2613.911 Da / Num. of mol.: 1 / Fragment: UNP residues 609-633
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: RTS / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JNX8, UniProt: B1WBC8*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D 1H
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1412D 1H-1H TOCSY
1512D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.1 mM RecQ4 zinc knuckle-1, 1.25 mM ZnCl2-2, 10 % D2O-3, 20 mM sodium phosphate pH 6.3-4, 150 mM potassium chloride-5, 4 mM DTT-6, 0.3 mM DSS-7, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.1 mMRecQ4 zinc knuckle-11
1.25 mMZnCl2-21
10 %D2O-31
20 mMsodium phosphate pH 6.3-41
150 mMpotassium chloride-51
4 mMDTT-61
0.3 mMDSS-71
Sample conditionsIonic strength: 170 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
CcpNMR2.5.1CCPNchemical shift assignment
CcpNMR2.5.1CCPNpeak picking
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3.1Linge, O'Donoghue and Nilgesrefinement
TALOSCornilescu, Delaglio and Baxdihedral angle calculations
ProcheckNMRLaskowski and MacArthurgeometry optimization
ProcheckNMRLaskowski and MacArthurrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 167 / NOE intraresidue total count: 87 / NOE long range total count: 9 / NOE medium range total count: 22 / NOE sequential total count: 49 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 7 / Protein psi angle constraints total count: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.137 Å / Distance rms dev error: 0.01 Å

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