ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / RNA-DNA hybrid ribonuclease activity ...ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / RNA-DNA hybrid ribonuclease activity / gene expression / fibroblast proliferation / in utero embryonic development / negative regulation of gene expression / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function
Histone, subunit A - #120 / N-terminal domain of TfIIb - #530 / Lipocalin - #680 / Ribonuclease H2, subunit C / Ribonuclease H2 non-catalytic subunit (Ylr154p-like) / Ribonuclease H2 subunit B, wHTH domain / Ribonuclease H2 subunit B / Rnh202, triple barrel domain / Ydr279p protein family (RNase H2 complex component) wHTH domain / Ydr279p protein triple barrel domain ...Histone, subunit A - #120 / N-terminal domain of TfIIb - #530 / Lipocalin - #680 / Ribonuclease H2, subunit C / Ribonuclease H2 non-catalytic subunit (Ylr154p-like) / Ribonuclease H2 subunit B, wHTH domain / Ribonuclease H2 subunit B / Rnh202, triple barrel domain / Ydr279p protein family (RNase H2 complex component) wHTH domain / Ydr279p protein triple barrel domain / Ribonuclease hii. Domain 2 / Ribonuclease H2, subunit A / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease (RNase) H type-2 domain profile. / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Histone, subunit A / N-terminal domain of TfIIb / Single Sheet / Ribonuclease H-like superfamily/Ribonuclease H / Lipocalin / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
THIS ENTRY 3P5J REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3KIOSF DETERMINED ...THIS ENTRY 3P5J REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3KIOSF DETERMINED BY AUTHORS OF THE PDB ENTRY 3KIO: N.Shaban,D.Harvey,F.W.Perrino,T.Hollis.
Method to determine structure: MAD / Resolution: 2.9→24.61 Å / Cor.coef. Fo:Fc: 0.8969 / Cor.coef. Fo:Fc free: 0.8348 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: This is a re-refinement of the murine RNase H2 coordinates previously deposited by Shaban et al., 2010 (PDB ID 3KIO)
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2716
925
5.2 %
RANDOM
Rwork
0.21
-
-
-
obs
0.2132
17777
-
-
Displacement parameters
Biso mean: 62.48 Å2
Baniso -1
Baniso -2
Baniso -3
1-
13.0671 Å2
0 Å2
0 Å2
2-
-
-4.4747 Å2
0 Å2
3-
-
-
-8.5923 Å2
Refine analyze
Luzzati coordinate error obs: 0.405 Å
Refinement step
Cycle: LAST / Resolution: 2.9→24.61 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4016
0
0
0
4016
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.011
4116
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.28
5614
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1269
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
68
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
630
HARMONIC
5
X-RAY DIFFRACTION
t_it
4116
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.09
X-RAY DIFFRACTION
t_other_torsion
21.53
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
548
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
4644
4
LS refinement shell
Resolution: 2.9→3.08 Å / Total num. of bins used: 9
Rfactor
Num. reflection
% reflection
Rfree
0.2934
163
5.8 %
Rwork
0.229
2649
-
all
0.2326
2812
-
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
1.1145
-0.2948
0.7102
1.2523
-0.5222
2.3424
-0.0432
-0.0372
-0.1281
0.0149
0.0176
-0.0206
-0.0651
0.1222
0.0257
0.1858
-0.0251
-0.0022
-0.2376
-0.0287
-0.304
73.2007
9.6824
22.1632
2
5.9326
2.5634
-0.1113
0.0013
-0.3888
0.4014
-0.023
0.1306
-0.1646
-0.1336
0.0269
0.5442
0.0586
-0.3411
-0.004
-0.304
-0.0503
-0.042
-0.2907
-0.0841
0.304
22.3709
-7.1893
3.4824
3
4.5519
0.2111
0.9306
3.6213
0.8695
1.5601
0.1005
0.2979
-0.4617
-0.1266
-0.0983
0.5442
0.197
-0.1822
-0.0021
0.0704
-0.0255
-0.0155
-0.2576
-0.0167
-0.1683
45.4622
-2.7782
4.2073
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{ A|* }
A
10 - 299
2
X-RAY DIFFRACTION
2
{ B|* }
B
11 - 231
3
X-RAY DIFFRACTION
3
{ C|* }
C
14 - 162
+
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