- PDB-5m1x: Crystal structure of S. cerevisiae Rfa1 N-OB domain mutant (K45E) -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5m1x
Title
Crystal structure of S. cerevisiae Rfa1 N-OB domain mutant (K45E)
Components
Replication factor A protein 1
Keywords
REPLICATION / OB fold
Function / homology
Function and homology information
heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / telomere maintenance via recombination / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Translesion synthesis by REV1 ...heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / telomere maintenance via recombination / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / single-stranded telomeric DNA binding / Activation of ATR in response to replication stress / mitotic recombination / Termination of translesion DNA synthesis / reciprocal meiotic recombination / DNA unwinding involved in DNA replication / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / Dual incision in TC-NER / telomere maintenance via telomerase / telomere maintenance / condensed nuclear chromosome / nucleotide-excision repair / double-strand break repair via homologous recombination / establishment of protein localization / single-stranded DNA binding / double-stranded DNA binding / DNA replication / sequence-specific DNA binding / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / mRNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding, OB-fold Similarity search - Domain/homology
ReplicationfactorAprotein1 / RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / ...RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / Single-stranded DNA-binding protein
Mass: 15616.754 Da / Num. of mol.: 4 / Mutation: K45E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: RFA1, BUF2, RPA1, YAR007C, FUN3 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22336
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979 Å / Relative weight: 1
Reflection
Resolution: 1.8→44.26 Å / Num. obs: 80762 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 23.08 Å2 / CC1/2: 0.99 / Rsym value: 0.079 / Net I/σ(I): 8.02
Reflection shell
Resolution: 1.8→1.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.74 / CC1/2: 0.68 / % possible all: 86.2
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Processing
Software
Name
Version
Classification
BUSTER
2.11.5
refinement
XDS
datareduction
XSCALE
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.8→44.26 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.9243 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.129 Details: Experimental details report unique reflections for unmerged Friedel pairs. Refinement was carried out on the same data with merged Friedel pairs. Automatic form factor correction at 0.97941 ...Details: Experimental details report unique reflections for unmerged Friedel pairs. Refinement was carried out on the same data with merged Friedel pairs. Automatic form factor correction at 0.97941 A was used for Se atoms in Buster.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2136
2086
5 %
RANDOM
Rwork
0.1644
-
-
-
obs
0.1669
41721
97.36 %
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Displacement parameters
Biso mean: 31.72 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.6259 Å2
0 Å2
-0.994 Å2
2-
-
-8.2269 Å2
0 Å2
3-
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5.601 Å2
Refine analyze
Luzzati coordinate error obs: 0.209 Å
Refinement step
Cycle: 1 / Resolution: 1.8→44.26 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4246
0
0
407
4653
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
4321
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.05
5833
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1579
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
135
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
626
HARMONIC
5
X-RAY DIFFRACTION
t_it
4321
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.21
X-RAY DIFFRACTION
t_other_torsion
16.96
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
564
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
5419
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.8→1.85 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2387
141
4.97 %
Rwork
0.1995
2695
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all
0.2015
2836
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obs
-
-
97.36 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.8306
0.2422
-0.4453
0.8045
-0.5031
1.6475
0.0571
-0.0417
0.2737
0.0512
0.007
0.0495
0.0325
0.0265
-0.0641
-0.0848
0.0153
-0.0142
-0.0261
0.0161
-0.0008
23.2152
85.1645
8.7282
2
2.0603
-0.2892
-0.7485
1.2482
0.2543
1.9899
-0.0881
-0.3714
0.1716
0.1323
0.1612
0.023
0.0399
0.0914
-0.0731
-0.1014
0.0103
-0.0209
-0.0077
-0.0705
-0.0254
17.904
32.2151
18.8834
3
1.319
-0.3184
0.3203
1.3116
-0.5605
2.171
0.0935
0.127
-0.1269
-0.1069
0.0632
0.0988
0.0755
-0.0336
-0.1567
-0.0632
0.0064
-0.0515
-0.0299
-0.0056
-0.0246
21.0093
62.3237
26.092
4
3.2043
0.7351
0.1421
1.8608
-0.7954
2.0836
0.102
-0.5447
-0.2436
0.2188
-0.1146
-0.1583
-0.1303
0.1879
0.0126
-0.0956
-0.0167
-0.0603
-0.0266
0.0467
-0.0757
10.7903
58.9436
-15.0668
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|* }
2
X-RAY DIFFRACTION
2
{ B|* }
3
X-RAY DIFFRACTION
3
{ C|* }
4
X-RAY DIFFRACTION
4
{ D|* }
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