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- PDB-2ma3: NMR solution structure of the C-terminus of the minichromosome ma... -

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Basic information

Entry
Database: PDB / ID: 2ma3
TitleNMR solution structure of the C-terminus of the minichromosome maintenance protein MCM from Methanothermobacter thermautotrophicus
ComponentsDNA replication initiator (Cdc21/Cdc54)
KeywordsREPLICATION / Minichromosome maintenance protein / MCM / Winged helix
Function / homology
Function and homology information


MCM complex / DNA replication initiation / DNA helicase activity / DNA helicase / hydrolase activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
: / Archaeal MCM, winged-helix / Mini-chromosome maintenance complex protein 4 / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain ...: / Archaeal MCM, winged-helix / Mini-chromosome maintenance complex protein 4 / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model15
AuthorsWiedemann, C. / Ohlenschlager, O. / Medagli, B. / Onesti, S. / Gorlach, M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex.
Authors: Wiedemann, C. / Szambowska, A. / Hafner, S. / Ohlenschlager, O. / Guhrs, K.H. / Gorlach, M.
History
DepositionJun 26, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jun 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 1.3May 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: DNA replication initiator (Cdc21/Cdc54)


Theoretical massNumber of molelcules
Total (without water)10,1361
Polymers10,1361
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA replication initiator (Cdc21/Cdc54)


Mass: 10135.653 Da / Num. of mol.: 1 / Fragment: UNP residues 583-666
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: ATCC 29096 / Gene: MTH_1770 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RILP / References: UniProt: O27798

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D HNCO
1613D HCACO
1713D HNHA
1813D C(CO)NH
1913D H(CCO)NH
11013D 1H-15N TOCSY
11123D 1H-13C NOESY aliphatic
11223D 1H-13C NOESY aromatic
11313D 1H-13C NOESY aliphatic
11413D 1H-15N NOESY
11512D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] C-terminus of the minichromosome maintenance protein MCM of Methanothermobacter thermautotrophicus, 10 mM sodium phosphate, 150 mM sodium chloride, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] C-terminus of the minichromosome maintenance protein MCM of Methanothermobacter thermautotrophicus, 10 mM sodium phosphate, 150 mM sodium chloride, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC-terminus of the minichromosome maintenance protein MCM of Methanothermobacter thermautotrophicus-1[U-13C; U-15N]1
10 mMsodium phosphate-21
150 mMsodium chloride-31
90 %H2O-41
10 %D2O-51
1 mMC-terminus of the minichromosome maintenance protein MCM of Methanothermobacter thermautotrophicus-6[U-13C; U-15N]2
10 mMsodium phosphate-72
150 mMsodium chloride-82
100 %D2O-92
Sample conditionsIonic strength: 160 / pH: 6.2 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Bruker AvanceIII / Manufacturer: Bruker / Model: AVANCE III / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNdata analysis
CYANArefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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