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- PDB-7tl2: Crystal Structure of Yeast p58C Multi-Tyrosine Mutant 5YF412 -

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Basic information

Entry
Database: PDB / ID: 7tl2
TitleCrystal Structure of Yeast p58C Multi-Tyrosine Mutant 5YF412
ComponentsDNA primase large subunit
KeywordsREPLICATION / 4Fe-4S cluster / DNA binding
Function / homologyIRON/SULFUR CLUSTER / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.529 Å
AuthorsBlee, A.M. / Salay, L.E. / Chazin, W.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118089 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA009582 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM80320 United States
CitationJournal: Biochemistry / Year: 2022
Title: Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase.
Authors: Salay, L.E. / Blee, A.M. / Raza, M.K. / Gallagher, K.S. / Chen, H. / Dorfeuille, A.J. / Barton, J.K. / Chazin, W.J.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1487
Polymers23,2831
Non-polymers8646
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.624, 51.870, 89.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA primase large subunit


Mass: 23283.309 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: Y352F, Y353F, Y395F, Y397F, Y412F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS3693 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7I9C0U2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Protein drops contained 20 mM HEPES (pH 6.8), 75 mM NaCl, 2 mM DTT mixed with equal volume of 100 mM TRIS (pH 8.5) and 55-70% MPD.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.529→30 Å / Num. obs: 29249 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.018 / Rrim(I) all: 0.043 / Χ2: 1.045 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.585.10.35328010.9450.1690.3920.87498.1
1.58-1.655.80.26328710.9750.1190.2890.913100
1.65-1.7260.19728970.9850.0880.2160.963100
1.72-1.8160.13728850.9930.0610.151.017100
1.81-1.9360.09529220.9960.0420.1041.079100
1.93-2.086.10.06728980.9980.030.0741.14100
2.08-2.296.10.04829350.9980.0210.0521.032100
2.29-2.626.10.04229310.9990.0190.0461.083100
2.62-3.2960.03429860.9990.0150.0371.187100
3.29-305.70.02631230.9990.0120.0281.10999.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.03 Å26.02 Å
Translation5.03 Å26.02 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTZ

6dtz


Resolution: 1.529→26.018 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.168 1458 5 %
Rwork0.1516 27727 -
obs0.1524 29185 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.26 Å2 / Biso mean: 26.9882 Å2 / Biso min: 11.92 Å2
Refinement stepCycle: final / Resolution: 1.529→26.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 42 89 1636
Biso mean--37.42 35.06 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141642
X-RAY DIFFRACTIONf_angle_d1.2072219
X-RAY DIFFRACTIONf_dihedral_angle_d6.9591338
X-RAY DIFFRACTIONf_chiral_restr0.074225
X-RAY DIFFRACTIONf_plane_restr0.009281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.53-1.58340.20111370.181260296
1.5834-1.64670.21071400.15292747100
1.6467-1.72170.18191450.13632748100
1.7217-1.81240.1581420.13422737100
1.8124-1.92590.1831360.12932789100
1.9259-2.07460.13321570.12922752100
2.0746-2.28320.151470.13412780100
2.2832-2.61340.16931470.14912789100
2.6134-3.29150.15541730.15532813100
3.2915-26.0180.18351340.1672297099
Refinement TLS params.Method: refined / Origin x: -16.1076 Å / Origin y: 1.2159 Å / Origin z: -14.6885 Å
111213212223313233
T0.1076 Å2-0.0135 Å2-0.006 Å2-0.1254 Å20.0036 Å2--0.1339 Å2
L0.4551 °2-0.1864 °20.0694 °2-1.1607 °20.1358 °2--1.2637 °2
S-0.0072 Å °-0.0318 Å °-0.0171 Å °-0.0079 Å °-0.0346 Å °-0.0053 Å °-0.0384 Å °0.0691 Å °-0.0541 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA316 - 512
2X-RAY DIFFRACTION1allA601 - 801
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allB1
5X-RAY DIFFRACTION1allB2
6X-RAY DIFFRACTION1allS1 - 123

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