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- PDB-7tl4: Crystal Structure of Yeast p58C Multi-Tyrosine Mutant 6YF -

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Basic information

Entry
Database: PDB / ID: 7tl4
TitleCrystal Structure of Yeast p58C Multi-Tyrosine Mutant 6YF
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: 1.805 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)23,7373
Polymers23,2671
Non-polymers4702
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.519, 51.488, 90.027
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: 23267.309 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: Y352F, Y353F, Y395F, Y397F, Y412F, 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.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.97 Å3/Da / Density % sol: 37.51 %
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: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 16970 / % possible obs: 97 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.041 / Rrim(I) all: 0.095 / Χ2: 1.019 / Net I/σ(I): 13.7 / Num. measured all: 90999
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.864.40.33814890.9650.1720.3811.0187.5
1.86-1.944.80.30616470.9760.1510.3431.0396.2
1.94-2.035.30.26816960.9810.1260.2971.03798.5
2.03-2.135.60.20916990.9890.0960.2311.04498.8
2.13-2.275.80.16916930.9920.0770.1861.09599.2
2.27-2.445.70.13917490.9910.0640.1531.05499.2
2.44-2.695.80.1117170.9930.0520.1221.05299.3
2.69-3.085.60.0917580.9910.0440.1010.97899.4
3.08-3.885.30.0717240.9920.0350.0790.98197.9
3.88-305.20.06417980.990.0310.0710.90194.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.99 Å29.61 Å
Translation4.99 Å29.61 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: 1.805→29.606 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 875 5.17 %
Rwork0.1962 16051 -
obs0.1971 16926 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.97 Å2 / Biso mean: 40.6517 Å2 / Biso min: 22.94 Å2
Refinement stepCycle: final / Resolution: 1.805→29.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 16 37 1508
Biso mean--32.69 40.24 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161543
X-RAY DIFFRACTIONf_angle_d1.2532094
X-RAY DIFFRACTIONf_dihedral_angle_d3.7411230
X-RAY DIFFRACTIONf_chiral_restr0.087220
X-RAY DIFFRACTIONf_plane_restr0.01267
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.805-1.91770.25081400.2332238088
1.9177-2.06580.27571430.2213266998
2.0658-2.27360.22921460.1957269599
2.2736-2.60240.2371500.1938274299
2.6024-3.27810.23371530.2098276299
3.2781-29.6060.18061430.1821280396
Refinement TLS params.Method: refined / Origin x: -15.7984 Å / Origin y: 1.2239 Å / Origin z: -14.6574 Å
111213212223313233
T0.188 Å2-0.0454 Å2-0.0047 Å2-0.2315 Å20.0177 Å2--0.2725 Å2
L1.1406 °2-0.2903 °20.7101 °2-3.1254 °20.8004 °2--4.6837 °2
S0.0949 Å °-0.0266 Å °-0.0489 Å °-0.1309 Å °-0.1425 Å °-0.0186 Å °0.0398 Å °0.057 Å °0.0543 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA316 - 512
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allD1 - 37

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