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- PDB-4ywl: Pyrococcus furiosus MCM N-terminal domain F179A point mutant pent... -

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Basic information

Entry
Database: PDB / ID: 4ywl
TitlePyrococcus furiosus MCM N-terminal domain F179A point mutant pentameric ring
ComponentsCell division control protein 21
KeywordsCELL CYCLE / MCM / helicase / replication / OB-fold
Function / homology
Function and homology information


intein-mediated protein splicing / MCM complex / single-stranded DNA helicase activity / single-stranded DNA binding / endonuclease activity / DNA helicase / 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: 3.2 Å
AuthorsFroelich, C.A. / Enemark, E.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098771 United States
St. Jude Children's Research Hospital (ALSAC) United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: MCM ring hexamerization is a prerequisite for DNA-binding.
Authors: Froelich, C.A. / Nourse, A. / Enemark, E.J.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
G: Cell division control protein 21
H: Cell division control protein 21
I: Cell division control protein 21
J: Cell division control protein 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,76529
Polymers293,24610
Non-polymers1,51919
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
G: Cell division control protein 21
H: Cell division control protein 21
I: Cell division control protein 21
J: 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
G: Cell division control protein 21
H: Cell division control protein 21
I: Cell division control protein 21
J: Cell division control protein 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)589,53058
Polymers586,49220
Non-polymers3,03738
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area52000 Å2
ΔGint-410.1 kcal/mol
Surface area235120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.018, 213.018, 213.978
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
12F
22G
32H
42I
52J

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALSERSERAA1 - 2532 - 254
211VALVALSERSERBB1 - 2532 - 254
311VALVALSERSERCC1 - 2532 - 254
411VALVALSERSERDD1 - 2532 - 254
511VALVALSERSEREE1 - 2532 - 254
112VALVALASPASPFF1 - 322 - 33
212VALVALASPASPGG1 - 322 - 33
312VALVALASPASPHH1 - 322 - 33
412VALVALASPASPII1 - 322 - 33
512VALVALASPASPJJ1 - 322 - 33
122ARGARGSERSERFF40 - 25341 - 254
222ARGARGSERSERGG40 - 25341 - 254
322ARGARGSERSERHH40 - 25341 - 254
422ARGARGSERSERII40 - 25341 - 254
522ARGARGSERSERJJ40 - 25341 - 254

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.311132, -0.950215, 0.016976), (0.950355, 0.31099, -0.010499), (0.004697, 0.0194, 0.999801)-59.94033, -135.84558, 2.11531
3given(-0.808622, -0.588104, 0.016277), (0.588297, -0.808556, 0.011972), (0.00612, 0.019256, 0.999796)50.54793, -235.04121, 1.63246
4given(-0.810036, 0.586186, 0.015045), (-0.58626, -0.810122, -0.000629), (0.011819, -0.00933, 0.999887)179.2932, -161.11708, -1.42856
5given(0.304683, 0.952408, 0.009375), (-0.952355, 0.304496, 0.017369), (0.013688, -0.01422, 0.999805)148.76613, -15.35245, -2.35604
6given(1), (1), (1)
7given(0.303299, -0.952449, 0.029154), (0.952838, 0.302802, -0.02028), (0.010488, 0.03393, 0.999369)-59.63505, -137.09776, 3.9462
8given(-0.809956, -0.586419, 0.009115), (0.586458, -0.809977, 0.002082), (0.006162, 0.007032, 0.999956)50.51984, -235.2601, 0.50675
9given(-0.806951, 0.589818, 0.030739), (-0.590432, -0.806909, -0.016939), (0.014812, -0.031818, 0.999384)179.7495, -160.84369, -3.17425
10given(0.310361, 0.950612, 0.003648), (-0.950381, 0.310367, -0.021192), (-0.021278, 0.00311, 0.999769)147.88457, -15.60733, 3.35579
DetailsThe biological assembly for the wild-type protein is a hexamer by analytical ultracentrifugation. But the F179A mutation disrupts hexamerization to produce an assembly that is presumed to be non-biological. A pentameric ring flanked by 5 peripheral monomers is observed in the crystal structure.

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Components

#1: Protein
Cell division control protein 21


Mass: 29324.617 Da / Num. of mol.: 10 / Mutation: F179A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0482 / 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.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.78 Å3/Da / Density % sol: 74.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate, pH 6.5, 1 mM spermine, 35 mM MgCl2, 2.45 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 92894 / Num. obs: 92894 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rsym value: 0.192 / Net I/σ(I): 13
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.6 / % 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: 3.2→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.905 / SU B: 16.363 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.574 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22988 4633 5 %RANDOM
Rwork0.2023 ---
obs0.20367 87902 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å2-0 Å2
2---0.32 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20310 0 55 0 20365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01920726
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.97627984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.13152530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85524.6531010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.077153880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.99115160
X-RAY DIFFRACTIONr_chiral_restr0.0740.23189
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115470
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.372 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 655 -
Rwork0.312 12543 -
obs--99.03 %

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