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- PDB-2kwq: Mcm10 C-terminal DNA binding domain -

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Basic information

Entry
Database: PDB / ID: 2kwq
TitleMcm10 C-terminal DNA binding domain
ComponentsProtein MCM10 homolog
KeywordsDNA BINDING PROTEIN / Mcm10 / DNA replication / DNA binding / Zinc motif / Zinc ribbon
Function / homology
Function and homology information


nuclear replication fork / DNA replication origin binding / DNA replication initiation / single-stranded DNA binding / DNA damage response / zinc ion binding / nucleus
Similarity search - Function
Replication factor Mcm10, C-terminal / : / : / Mcm10, C-terminal zinc binding motif / Mcm10, CCCH-type zinc motif / Mcm10 replication factor / Zinc finger, Mcm10/DnaG-type / Minichromosome maintenance protein 10 / Primase zinc finger / MCM10 OB-fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Protein MCM10 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 3
AuthorsRobertson, P.D. / Chagot, B. / Chazin, W.J. / Eichman, B.F.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Solution NMR structure of the C-terminal DNA binding domain of Mcm10 reveals a conserved MCM motif.
Authors: Robertson, P.D. / Chagot, B. / Chazin, W.J. / Eichman, B.F.
History
DepositionApr 15, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: pdbx_database_status / pdbx_nmr_sample_details ...pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_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_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: Protein MCM10 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7273
Polymers10,5961
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein MCM10 homolog


Mass: 10596.490 Da / Num. of mol.: 1
Fragment: C-terminal DNA binding domain (UNP residues 755-842)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: mcm10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EAW4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1352D 1H-1H TOCSY
1452D 1H-1H NOESY
1552D 1H-1H COSY
1643D CBCA(CO)NH
1743D HNCO
1843D HN(CA)CB
1943D HBHA(CO)NH
11013D HNHA
11143D H(CCO)NH
11243D C(CO)NH
11313D 1H-15N NOESY
11433D 1H-13C NOESY
11513D (HB)CB(CGCD)HD

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Sample preparation

Details
Solution-IDContentsSolvent system
1920 uM [U-100% 15N] entity_1-1, 25 mM sodium phosphate-2, 100 mM sodium chloride-3, 5 % D2O-4, 95 % H2O-5, 95% H2O/5% D2O95% H2O/5% D2O
2300 uM [U-100% 15N] entity_1-6, 25 mM sodium phosphate-7, 100 mM sodium chloride-8, 5 % D2O-9, 95 % H2O-10, 95% H2O/5% D2O95% H2O/5% D2O
3920 uM [U-100% 13C] entity_1-11, 25 mM sodium phosphate-12, 100 mM sodium chloride-13, 5 % D2O-14, 95 % H2O-15, 95% H2O/5% D2O95% H2O/5% D2O
4920 uM [U-100% 13C; U-100% 15N] entity_1-16, 25 mM sodium phosphate-17, 100 mM sodium chloride-18, 5 % D2O-19, 95 % H2O-20, 95% H2O/5% D2O95% H2O/5% D2O
5920 uM entity_1-21, 25 mM sodium phosphate-22, 100 mM sodium chloride-23, 5 % D2O-24, 95 % H2O-25, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
920 uMentity_1-1[U-100% 15N]1
25 mMsodium phosphate-21
100 mMsodium chloride-31
5 %D2O-41
95 %H2O-51
300 uMentity_1-6[U-100% 15N]2
25 mMsodium phosphate-72
100 mMsodium chloride-82
5 %D2O-92
95 %H2O-102
920 uMentity_1-11[U-100% 13C]3
25 mMsodium phosphate-123
100 mMsodium chloride-133
5 %D2O-143
95 %H2O-153
920 uMentity_1-16[U-100% 13C; U-100% 15N]4
25 mMsodium phosphate-174
100 mMsodium chloride-184
5 %D2O-194
95 %H2O-204
920 uMentity_1-215
25 mMsodium phosphate-225
100 mMsodium chloride-235
5 %D2O-245
95 %H2O-255
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: restrained molecular dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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