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- PDB-7tl3: Crystal Structure of Yeast p58C Multi-Tyrosine Mutant 5YF431 -

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Basic information

Entry
Database: PDB / ID: 7tl3
TitleCrystal Structure of Yeast p58C Multi-Tyrosine Mutant 5YF431
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: 2.066 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)23,8714
Polymers23,2831
Non-polymers5883
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.044, 51.097, 90.223
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, Y431F
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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.03 Å3/Da / Density % sol: 39.46 %
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-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.05→30.359 Å / Num. obs: 11722 / % possible obs: 96.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.078 / Rrim(I) all: 0.166 / Χ2: 1 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.123.40.47310110.8870.2720.5491.06885
2.12-2.213.80.40911040.9320.2260.4691.05394
2.21-2.314.30.42111520.9310.2250.4790.9997.5
2.31-2.434.90.39911800.9550.1990.4481.04399.6
2.43-2.585.30.34212020.9440.1680.3830.99299.9
2.58-2.785.50.27811850.970.1340.310.99899.7
2.78-3.065.50.21312070.9810.1050.2381.01699.9
3.06-3.55.40.15812100.9720.080.1780.92999.8
3.5-4.415.30.10612290.9840.0550.120.93198.9
4.41-304.50.10412420.9790.0610.1221.0593.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.97 Å30.36 Å
Translation4.97 Å30.36 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: 2.066→30.359 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 1165 9.99 %
Rwork0.2356 10492 -
obs0.2397 11657 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.3 Å2 / Biso mean: 42.8526 Å2 / Biso min: 26 Å2
Refinement stepCycle: final / Resolution: 2.066→30.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 24 19 1525
Biso mean--49.48 41.9 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031571
X-RAY DIFFRACTIONf_angle_d0.4942126
X-RAY DIFFRACTIONf_dihedral_angle_d3.3291271
X-RAY DIFFRACTIONf_chiral_restr0.037220
X-RAY DIFFRACTIONf_plane_restr0.003270
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0663-2.16040.37921200.2919109482
2.1604-2.27420.32991390.2662125394
2.2742-2.41670.30531500.2654133799
2.4167-2.60310.29621480.24661337100
2.6031-2.86490.31211490.25411350100
2.8649-3.27910.31541500.247135599
3.2791-4.12960.25981550.207138799
4.1296-30.3590.23361540.2257137994
Refinement TLS params.Method: refined / Origin x: 4.3149 Å / Origin y: 24.6325 Å / Origin z: 14.3569 Å
111213212223313233
T0.5137 Å20.0399 Å20.0349 Å2-0.2196 Å2-0.0003 Å2--0.2246 Å2
L0.9952 °20.205 °2-0.6584 °2-0.8363 °20.0969 °2--1.8915 °2
S0.0211 Å °0.1203 Å °0.0559 Å °-0.1013 Å °-0.0703 Å °-0.0077 Å °0.0754 Å °-0.0284 Å °0.0647 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA316 - 512
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allB1 - 3
4X-RAY DIFFRACTION1allD1 - 19

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