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- PDB-1ltl: THE DODECAMER STRUCTURE OF MCM FROM ARCHAEAL M. THERMOAUTOTROPHICUM -

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Basic information

Entry
Database: PDB / ID: 1ltl
TitleTHE DODECAMER STRUCTURE OF MCM FROM ARCHAEAL M. THERMOAUTOTROPHICUM
ComponentsDNA replication initiator (Cdc21/Cdc54)
KeywordsREPLICATION
Function / homology
Function and homology information


MCM complex / single-stranded DNA helicase activity / DNA replication initiation / single-stranded DNA binding / DNA helicase / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
: / Archaeal MCM, winged-helix / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Rubrerythrin, domain 2 - #10 / Mini-chromosome maintenance complex protein 4 / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain ...: / Archaeal MCM, winged-helix / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Rubrerythrin, domain 2 - #10 / 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 / Rubrerythrin, domain 2 / Single Sheet / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, SAD / Resolution: 3 Å
AuthorsFletcher, R.J. / Bishop, B.E. / Leon, R.P. / Sclafani, R.A. / Ogata, C.M. / Chen, X.S.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: The Structure and function of MCM from archaeal M. Thermoautotrophicum
Authors: Fletcher, R.J. / Bishop, B.E. / Leon, R.P. / Sclafani, R.A. / Ogata, C.M. / Chen, X.S.
History
DepositionMay 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 22, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA replication initiator (Cdc21/Cdc54)
B: DNA replication initiator (Cdc21/Cdc54)
C: DNA replication initiator (Cdc21/Cdc54)
D: DNA replication initiator (Cdc21/Cdc54)
E: DNA replication initiator (Cdc21/Cdc54)
F: DNA replication initiator (Cdc21/Cdc54)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,41212
Polymers194,0206
Non-polymers3926
Water00
1
A: DNA replication initiator (Cdc21/Cdc54)
B: DNA replication initiator (Cdc21/Cdc54)
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)388,82524
Polymers388,04012
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
2
C: DNA replication initiator (Cdc21/Cdc54)
D: DNA replication initiator (Cdc21/Cdc54)
E: DNA replication initiator (Cdc21/Cdc54)
F: DNA replication initiator (Cdc21/Cdc54)
hetero molecules

C: DNA replication initiator (Cdc21/Cdc54)
D: DNA replication initiator (Cdc21/Cdc54)
E: DNA replication initiator (Cdc21/Cdc54)
F: DNA replication initiator (Cdc21/Cdc54)
hetero molecules

C: DNA replication initiator (Cdc21/Cdc54)
D: DNA replication initiator (Cdc21/Cdc54)
E: DNA replication initiator (Cdc21/Cdc54)
F: DNA replication initiator (Cdc21/Cdc54)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,82524
Polymers388,04012
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)192.321, 192.321, 365.539
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 32336.662 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: O27798
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growDetails: Hanging drop
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1reservoirpH8.0
20.8 Msodium citrate1reservoir
310 %(v/v)glycerol1reservoir
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 8, 2001
RadiationMonochromator: DOUBLE CRYSTAL SI-111, DOUBLE CRYSTAL SI-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→49.83 Å / Num. obs: 58151 / Observed criterion σ(I): -3
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. obs: 56524 / Num. measured all: 835966 / Rmerge(I) obs: 99.9 / Rmerge F obs: 0.095
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.47

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SIR, SAD / Resolution: 3→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.295 -RANDOM
Rwork0.245 --
all-53766 -
obs-53766 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11627 0 6 0 11633
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.021
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg4.207

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