- PDB-2xb0: DNA-binding domain from Saccharomyces cerevisiae chromatin- remod... -
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Basic information
Entry
Database: PDB / ID: 2xb0
Title
DNA-binding domain from Saccharomyces cerevisiae chromatin- remodelling protein Chd1
Components
CHROMO DOMAIN-CONTAINING PROTEIN 1
Keywords
HYDROLASE / DNA-BINDING PROTEIN / TRANSCRIPTION / CHROMATIN REGULATOR
Function / homology
Function and homology information
nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / sister chromatid cohesion / ATP-dependent chromatin remodeler activity ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SAGA complex / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / chromatin DNA binding / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Sequence details
PARTIAL SEQUENCE (AA 1009-1274) CORRESPONDING TO THE DNA- BINDING DOMAIN OF YEAST CHD1. FIRST FOUR ...PARTIAL SEQUENCE (AA 1009-1274) CORRESPONDING TO THE DNA- BINDING DOMAIN OF YEAST CHD1. FIRST FOUR RESIDUES (GPLG) ARE NON-NATIVE AND ARE LEFT FROM CLEAVAGE OF THE GST-TAG WITH PRESCISSION PROTEASE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.77 Å3/Da / Density % sol: 55.57 % / Description: NONE
Crystal grow
pH: 7.5 / Details: 0.1 M TRIS, PH 8.5, 28% PEG 4K, 0.35 M MGCL2
Resolution: 2→49.2 Å / Num. obs: 22943 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 34.64 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1
Reflection shell
Resolution: 2→2.11 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.5 / % possible all: 95.9
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
MOSFLM
datareduction
SCALA
datascaling
PHENIX
phasing
Refinement
Method to determine structure: MAD Starting model: NONE Resolution: 2→49.255 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML Details: RIDING HYDROGENS WERE USED IN REFINEMENT AMINO ACIDS 209-240 (NEVHNPVAKKSASSSDTTPTPSKKGKGITGSS) AND 266-270 (TKSPS) ARE DISORDERED WERE NOT MODELLED OWING TO INSUFFICIENT ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Rfree
0.2479
2263
9.9 %
Rwork
0.205
-
-
obs
0.2093
22894
97.18 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.114 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Biso mean: 61.3 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.8428 Å2
0 Å2
0 Å2
2-
-
5.0238 Å2
0 Å2
3-
-
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-6.8666 Å2
Refinement step
Cycle: LAST / Resolution: 2→49.255 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1842
0
14
109
1965
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.018
1938
X-RAY DIFFRACTION
f_angle_d
1.359
2598
X-RAY DIFFRACTION
f_dihedral_angle_d
14.263
752
X-RAY DIFFRACTION
f_chiral_restr
0.085
279
X-RAY DIFFRACTION
f_plane_restr
0.005
330
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2-2.0715
0.3591
208
0.327
1989
X-RAY DIFFRACTION
95
2.0715-2.1544
0.3008
208
0.2838
2026
X-RAY DIFFRACTION
98
2.1544-2.2525
0.3087
210
0.2413
2029
X-RAY DIFFRACTION
96
2.2525-2.3713
0.2817
233
0.2126
2002
X-RAY DIFFRACTION
96
2.3713-2.5198
0.2563
206
0.1984
2062
X-RAY DIFFRACTION
97
2.5198-2.7144
0.2583
248
0.1961
2021
X-RAY DIFFRACTION
98
2.7144-2.9875
0.2676
228
0.2091
2084
X-RAY DIFFRACTION
98
2.9875-3.4197
0.2662
246
0.2173
2072
X-RAY DIFFRACTION
98
3.4197-4.3081
0.2323
234
0.1754
2120
X-RAY DIFFRACTION
99
4.3081-49.2699
0.1995
242
0.1866
2226
X-RAY DIFFRACTION
97
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
0.5134
0.261
0.404
2.4028
2.0332
1.824
-0.0189
-0.1516
-0.0188
0.7428
0.1675
-0.2586
0.33
0.2885
-0.1368
0.4699
-0.0347
-0.0893
0.321
0.0324
0.2512
10.6756
65.3063
79.2636
2
2.3943
1.512
0.9081
3.2675
0.0964
0.8162
-0.2821
0.2469
-0.0041
-1.0554
0.3969
-0.0605
0.1143
0.0501
-0.0829
0.8428
-0.0351
-0.0412
0.3014
-0.0089
0.2257
-10.6744
34.2717
55.7702
3
2.3422
0.1727
2.3681
0.718
1.5019
5.1544
0.2534
-0.1417
-0.7285
0.0753
-0.6913
-0.1426
0.8482
-0.0586
0.1162
0.6494
-0.1447
-0.0506
0.3681
0.1101
0.3873
-1.2847
52.3863
74.4755
4
1.9885
0.9547
0.3068
1.3934
0.8226
1.8499
0.0822
-0.1246
0.632
0.0012
-0.1703
0.0882
-0.0359
-0.2246
0.1405
0.063
0.0027
-0.0073
0.1728
-0.1003
0.271
-1.831
75.6372
58.5856
5
0.9192
0.722
0.5578
0.6396
0.4402
0.406
0.3516
-1.4781
0.9828
0.3615
-0.8365
0.4929
0.1704
-0.7768
0.4399
0.1251
-0.166
0.0986
0.8782
-0.4324
0.5123
-15.494
75.1158
66.0314
6
1.6454
1.1824
-1.5309
2.2534
0.6436
3.7066
0.1182
-0.1278
-0.1652
0.3804
-0.3762
-0.2347
0.6517
-0.8418
0.2
0.1906
-0.1045
-0.0073
0.2784
-0.0336
0.2942
-4.3266
63.979
56.8805
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAINXANDRESID1:60)
2
X-RAY DIFFRACTION
2
(CHAINXANDRESID61:108)
3
X-RAY DIFFRACTION
3
(CHAINXANDRESID109:128)
4
X-RAY DIFFRACTION
4
(CHAINXANDRESID129:205)
5
X-RAY DIFFRACTION
5
(CHAINXANDRESID206:250)
6
X-RAY DIFFRACTION
6
(CHAINXANDRESID251:266)
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