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- PDB-4ywm: Pyrococcus furiosus MCM N-terminal domain beta-turn triple mutant... -

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Basic information

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


single-stranded 3'-5' DNA helicase activity / MCM complex / intein-mediated protein splicing / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / single-stranded DNA binding / endonuclease activity / DNA helicase / 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 / MCM N-terminal domain / MCM N-terminal domain / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / 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 / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / 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 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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)293,40728
Polymers291,98410
Non-polymers1,42318
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)586,81356
Polymers583,96820
Non-polymers2,84536
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area49530 Å2
ΔGint-369.9 kcal/mol
Surface area233690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.709, 210.709, 209.638
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:

Component-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 1 - 253 / Label seq-ID: 2 - 254

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
31CC
41DD
51EE
12FF
22GG
32HH
42II
52JJ

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.305243, -0.952138, 0.01612), (0.952274, 0.305188, -0.005839), (0.00064, 0.017133, 0.999853)-59.23452, -135.68381, 2.05504
3given(-0.805957, -0.591756, 0.016064), (0.591954, -0.805856, 0.013658), (0.004863, 0.020517, 0.999778)49.76168, -232.68259, 1.9675
4given(-0.807211, 0.590162, 0.010969), (-0.590206, -0.807252, -0.001108), (0.0082, -0.007369, 0.999939)177.67867, -159.48032, -1.07562
5given(0.30113, 0.95349, 0.013328), (-0.953541, 0.300956, 0.013592), (0.008949, -0.016802, 0.999819)148.14366, -15.7488, -2.10703
6given(1), (1), (1)
7given(0.33419, -0.942382, 0.015276), (0.942428, 0.334327, 0.007381), (-0.012063, 0.01193, 0.999856)-58.46892, -131.57449, 1.74047
8given(-0.806892, -0.590694, -0.002633), (0.590615, -0.806844, 0.013333), (-0.01, 0.009203, 0.999908)49.42288, -232.73938, 1.35659
9given(-0.823289, 0.567452, 0.013889), (-0.567386, -0.823406, 0.008723), (0.016386, -0.000699, 0.999866)177.62164, -162.51154, -1.18446
10given(0.290956, 0.95662, -0.01492), (-0.956573, 0.291159, 0.013952), (0.017691, 0.010213, 0.999791)149.20464, -16.57924, 0.02471
DetailsThe biological assembly for the wild-type protein is a hexamer. The beta turn triple mutant is a pentamer in solution by analytical ultracentrifugation. 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: 29198.395 Da / Num. of mol.: 10 / Mutation: K233A, R234A, K236A
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.: 8 / 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: 4.6 Å3/Da / Density % sol: 73.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100 mM Bis-Tris, pH 5.5, 1.75 M ammonium sulfate

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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: Dec 12, 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. obs: 88667 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Rsym value: 0.135 / Net I/σ(I): 18
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.9 / % 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: 0.904 / Cor.coef. Fo:Fc free: 0.874 / SU B: 19.31 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.757 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26962 4328 5 %RANDOM
Rwork0.23743 ---
obs0.23902 82414 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20255 0 50 0 20305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01920677
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220135
X-RAY DIFFRACTIONr_angle_refined_deg1.441.97327953
X-RAY DIFFRACTIONr_angle_other_deg0.8643.00246395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00152535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39524.7521010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.214153780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.27615150
X-RAY DIFFRACTIONr_chiral_restr0.0680.23193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02123095
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024415
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→3.373 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.367 636 -
Rwork0.338 12037 -
obs-12037 99.19 %

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