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- PDB-5iy0: PfMCM N-terminal domain double hexamer -

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Basic information

Entry
Database: PDB / ID: 5iy0
TitlePfMCM N-terminal domain double hexamer
ComponentsCell division control protein 21
KeywordsREPLICATION DNA BINDING PROTEIN / REPLICATION / DNA BINDING PROTEIN
Function / homology
Function and homology information


intein-mediated protein splicing / MCM complex / single-stranded DNA binding / endonuclease activity / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication ...intein-mediated protein splicing / MCM complex / single-stranded DNA binding / endonuclease activity / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / cell division / ATP binding / metal ion binding
Similarity search - Function
mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Rubrerythrin, domain 2 - #10 / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal ...mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Rubrerythrin, domain 2 - #10 / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / 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 speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMeagher, M. / Enemark, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM098771 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structure of a double hexamer of the Pyrococcus furiosus minichromosome maintenance protein N-terminal domain.
Authors: Meagher, M. / Enemark, E.J.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 21
B: Cell division control protein 21
C: Cell division control protein 21
D: Cell division control protein 21
E: Cell division control protein 21
F: Cell division control protein 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,79712
Polymers176,4046
Non-polymers3926
Water00
1
A: Cell division control protein 21
B: Cell division control protein 21
C: Cell division control protein 21
D: Cell division control protein 21
E: Cell division control protein 21
F: Cell division control protein 21
hetero molecules

A: Cell division control protein 21
B: Cell division control protein 21
C: Cell division control protein 21
D: Cell division control protein 21
E: Cell division control protein 21
F: Cell division control protein 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,59324
Polymers352,80912
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)211.427, 122.610, 111.892
Angle α, β, γ (deg.)90.00, 92.35, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 254
2111B1 - 254
3111C1 - 254
4111D1 - 254
5111E1 - 254
6111F1 - 254

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.501683, 0.864997, -0.009748), (-0.865043, 0.501696, -0.001246), (0.003813, 0.009057, 0.999952)-63.13068, 36.69931, -0.41282
3given(-0.497629, 0.867382, -0.003676), (-0.867386, -0.497609, 0.005084), (0.002581, 0.005719, 0.99998)-63.48684, 109.7942, -0.23775
4given(-0.999994, 0.000869, -0.003227), (-0.000863, -0.999998, -0.001874), (-0.003229, -0.001871, 0.999993)0.09623, 146.87088, 0.42166
5given(-0.502027, -0.864813, -0.008249), (0.864852, -0.502002, -0.004993), (0.000177, -0.009641, 0.999954)63.87112, 110.44051, 1.11535
6given(0.499108, -0.866539, -0.000957), (0.866539, 0.499109, -0.001007), (0.00135, -0.000327, 0.999999)63.70854, 36.68338, 0.20684

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Components

#1: Protein
Cell division control protein 21


Mass: 29400.711 Da / Num. of mol.: 6 / Fragment: N-terminal domain (UNP residues 2-256)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0482 / Plasmid: pRSFduet pLE009.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q8U3I4
#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: 4.11 Å3/Da / Density % sol: 70.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1 M HEPES, pH 7.1; 0.1 Magnesium Chloride; 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 57090 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.143 / Net I/av σ(I): 13 / Net I/σ(I): 6.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4POF

4pof


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.096 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.945 / ESU R Free: 0.323 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22273 2877 5 %RANDOM
Rwork0.20451 ---
obs0.20541 54114 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.029 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å2-0 Å21.12 Å2
2---2.08 Å2-0 Å2
3---5.44 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12186 0 6 0 12192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912396
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212162
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.97216740
X-RAY DIFFRACTIONr_angle_other_deg0.799328062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.32151512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21124.608612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98152328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7871596
X-RAY DIFFRACTIONr_chiral_restr0.0750.21902
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113824
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022664
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0985.0276066
X-RAY DIFFRACTIONr_mcbond_other3.0985.0266065
X-RAY DIFFRACTIONr_mcangle_it5.3247.5327572
X-RAY DIFFRACTIONr_mcangle_other5.3247.5327573
X-RAY DIFFRACTIONr_scbond_it2.9545.3166330
X-RAY DIFFRACTIONr_scbond_other2.9545.3176331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0617.8019169
X-RAY DIFFRACTIONr_long_range_B_refined8.61337.78613225
X-RAY DIFFRACTIONr_long_range_B_other8.61337.78913226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4046 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A3.97
B3
C2.73
D3.35
E3.22
F5.03
LS refinement shellResolution: 3→3.162 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 393 -
Rwork0.315 7641 -
obs--96.92 %

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