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- PDB-2m45: NMR solution structure of the C-terminus of the minichromosome ma... -

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Basic information

Entry
Database: PDB / ID: 2m45
TitleNMR solution structure of the C-terminus of the minichromosome maintenance protein MCM from Sulfolobus solfataricus
ComponentsMinichromosome maintenance protein MCM
KeywordsHYDROLASE / Minichromosome maintenance protein / MCM / Winged helix / helix-turn-helix / winged helix turn / DNA helicase / thermophile proteins / pre-replicative complex / replication
Function / homology
Function and homology information


MCM complex / DNA duplex unwinding / helicase activity / single-stranded DNA binding / DNA helicase / DNA replication / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
: / MCM protein C-terminal winged helix-turn-helix domain / 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 protein C-terminal winged helix-turn-helix domain / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Minichromosome maintenance protein MCM
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model3
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
DepositionJan 29, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minichromosome maintenance protein MCM


Theoretical massNumber of molelcules
Total (without water)9,6741
Polymers9,6741
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 Minichromosome maintenance protein MCM /


Mass: 9674.412 Da / Num. of mol.: 1 / Fragment: UNP residues 605-686
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / Gene: MCM, SSO0774 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9UXG1, DNA helicase

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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
1823D (H)CCH-COSY
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11123D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aliphatic
11323D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
1700 uM [U-100% 13C; U-100% 15N] C-terminus of the minichromosome maintenance protein MCM-1, 10 mM potassium phosphate-2, 150 mM sodium chloride-3, 0.05 w/v sodium azide-4, 90% H2O/10% D2O90% H2O/10% D2O
2700 uM [U-100% 13C; U-100% 15N] C-terminus of the minichromosome maintenance protein MCM-5, 10 mM potassium phosphate-6, 150 mM sodium chloride-7, 0.05 w/v sodium azide-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
700 uMC-terminus of the minichromosome maintenance protein MCM-1[U-100% 13C; U-100% 15N]1
10 mMpotassium phosphate-21
150 mMsodium chloride-31
0.05 w/vsodium azide-41
700 uMC-terminus of the minichromosome maintenance protein MCM-5[U-100% 13C; U-100% 15N]2
10 mMpotassium phosphate-62
150 mMsodium chloride-72
0.05 w/vsodium azide-82
Sample conditionsIonic strength: 160 / pH: 6.2 / Pressure: ambient / Temperature: 303 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection & processing
CcpNMRCCPNdata analysis
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
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 / Representative conformer: 3

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