- PDB-3m5b: Crystal structure of the BTB domain from FAZF/ZBTB32 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3m5b
Title
Crystal structure of the BTB domain from FAZF/ZBTB32
Components
Zinc finger and BTB domain-containing protein 32
Keywords
TRANSCRIPTION / BTB domain / POZ domain / BTB/POZ domain / ZBTB32 / Zinc finger and BTB domain-containing protein 32 / Fanconi anemia zinc finger protein / FAXF / Rog / TZFP / ZNF538 / Testis zinc finger protein / FANCC-interacting protein / transcription regulator / alpha/beta protein / PROTEIN-PROTEIN INTERACTION DOMAIN / ZINC-FINGER PROTEIN / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc-finger / DNA BINDING PROTEIN / FAZF
Function / homology
Function and homology information
chromatin => GO:0000785 / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Monochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979 Å / Relative weight: 1
Reflection
Resolution: 2→30 Å / Num. obs: 14434 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2.96 % / Rsym value: 0.063 / Net I/σ(I): 16.95
Reflection shell
Resolution: 2→2.05 Å / Mean I/σ(I) obs: 3.77 / Num. unique all: 953 / Rsym value: 0.245 / % possible all: 96.8
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Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
PHASER
phasing
REFMAC
5.2.0019
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: STARTING MODEL: SINGLE CHAIN POLY-ALANINE MODEL OF PDB CODE 1BUO, EXCEPT LOOP REGIONS AND TURNS
Resolution: 2→26.83 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.186 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24388
704
4.9 %
RANDOM
Rwork
0.18635
-
-
-
obs
0.18916
13726
99.22 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 24.46 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0.01 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 2→26.83 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1668
0
0
154
1822
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.022
1702
X-RAY DIFFRACTION
r_angle_refined_deg
1.792
1.981
2312
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.915
5
216
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
26.875
22.632
76
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.723
15
272
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.124
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.142
0.2
258
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1306
X-RAY DIFFRACTION
r_nbd_refined
0.216
0.2
538
X-RAY DIFFRACTION
r_nbtor_refined
0.295
0.2
1085
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.179
0.2
87
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.23
0.2
41
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.214
0.2
12
X-RAY DIFFRACTION
r_mcbond_it
1.383
1.5
1157
X-RAY DIFFRACTION
r_mcangle_it
1.931
2
1726
X-RAY DIFFRACTION
r_scbond_it
3.04
3
665
X-RAY DIFFRACTION
r_scangle_it
4.844
4.5
586
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.33
45
-
Rwork
0.203
1008
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obs
-
-
96.96 %
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