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- PDB-3ohu: Crystal structure of the human Bach2 POZ domain, form I -

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Basic information

Entry
Database: PDB / ID: 3ohu
TitleCrystal structure of the human Bach2 POZ domain, form I
ComponentsTranscription regulator protein BACH2
KeywordsTRANSCRIPTION / BTB/POZ domain
Function / homology
Function and homology information


primary adaptive immune response involving T cells and B cells / import into nucleus / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / 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 / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II ...primary adaptive immune response involving T cells and B cells / import into nucleus / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / 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 / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
BACH, basic leucine zipper (bZIP) domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper ...BACH, basic leucine zipper (bZIP) domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription regulator protein BACH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRosbrook, G.O. / Stead, M.A. / Carr, S.B. / Wright, S.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The structure of the Bach2 POZ-domain dimer reveals an intersubunit disulfide bond.
Authors: Rosbrook, G.O. / Stead, M.A. / Carr, S.B. / Wright, S.C.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription regulator protein BACH2
B: Transcription regulator protein BACH2
C: Transcription regulator protein BACH2
D: Transcription regulator protein BACH2
E: Transcription regulator protein BACH2
F: Transcription regulator protein BACH2


Theoretical massNumber of molelcules
Total (without water)85,6236
Polymers85,6236
Non-polymers00
Water4,972276
1
A: Transcription regulator protein BACH2
B: Transcription regulator protein BACH2


Theoretical massNumber of molelcules
Total (without water)28,5412
Polymers28,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-41 kcal/mol
Surface area12860 Å2
MethodPISA
2
C: Transcription regulator protein BACH2
F: Transcription regulator protein BACH2


Theoretical massNumber of molelcules
Total (without water)28,5412
Polymers28,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-37 kcal/mol
Surface area12350 Å2
MethodPISA
3
D: Transcription regulator protein BACH2
E: Transcription regulator protein BACH2


Theoretical massNumber of molelcules
Total (without water)28,5412
Polymers28,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-36 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.600, 96.970, 82.630
Angle α, β, γ (deg.)90.00, 101.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcription regulator protein BACH2 / BTB and CNC homolog 2


Mass: 14270.508 Da / Num. of mol.: 6 / Fragment: POZ domain, UNP residues 9-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Bach2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q9BYV9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulphate 0.1 M MES pH 5.5 4% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2009 / Details: mirrors
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→54.57 Å / Num. all: 50244 / Num. obs: 49842 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.093 / Rsym value: 0.112 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.872 / % possible all: 99.7

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ihc

2ihc


Resolution: 2.1→40.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.851 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25661 2529 5.1 %RANDOM
Rwork0.20987 ---
obs0.21231 47289 99.17 %-
all-50244 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å22.14 Å2
2---1.14 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5710 0 0 276 5986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9618055
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7145742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15923.132281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.071151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9971554
X-RAY DIFFRACTIONr_chiral_restr0.0860.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024455
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4311.53641
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83825887
X-RAY DIFFRACTIONr_scbond_it1.37732295
X-RAY DIFFRACTIONr_scangle_it2.3234.52162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 164 -
Rwork0.29 3539 -
obs--99.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.75540.82370.11072.43861.24080.9406-0.03170.04960.0112-0.03650.02220.1121-0.0227-0.01660.00940.35290.0127-0.04850.30740.03570.311718.7231.16646.467
21.88540.6439-1.17812.1629-0.08563.67710.15-0.22620.09530.2639-0.14020.21280.0766-0.1267-0.00980.308-0.0346-0.01730.32750.02860.281413.5054.65462.856
31.5770.242-0.40341.45581.86494.2125-0.14090.1024-0.0295-0.2988-0.0720.0462-0.08360.05470.21280.4548-0.0072-0.04640.2490.0280.318118.811-4.51941.39
41.81411.7610.4145.41450.2743.199-0.01790.2127-0.04-0.2057-0.0128-0.1098-0.4560.30180.03060.3525-0.0216-0.03820.28950.00920.301421.388-15.87932.912
52.97911.6744-2.33132.3798-1.94613.20810.3294-0.00530.23760.24880.01830.2386-0.36830.0811-0.34770.376-0.0030.06280.38380.01520.282616.459-0.9323.278
68.06332.76863.14826.01933.578110.98351.0298-0.43851.13820.6854-0.21831.1052-2.0217-0.3524-0.81150.99570.05790.77570.12310.08150.727812.55515.0555.478
72.0991-0.1375-1.27811.9717-0.33452.79790.08570.01210.0659-0.01040.0052-0.0614-0.09690.1437-0.09090.2962-0.0006-0.05790.3158-0.02210.3733-6.86220.48643.004
81.01630.1156-0.17863.3488-1.02252.4148-0.0844-0.0123-0.26860.19170.01270.01270.16730.03910.07180.31310.0291-0.03030.2867-0.02860.4431-8.4825.30247.928
91.43830.1162-0.09142.644-1.09881.456-0.00470.08640.1407-0.37760.0152-0.07650.03170.0801-0.01050.3263-0.02850.00920.2889-0.0450.3211-3.99728.29229.451
103.0382.1014-1.007214.7551-0.26630.36620.11870.3523-0.1913-1.2696-0.1915-0.7237-0.0346-0.05450.07280.47730.13860.13250.5043-0.00820.32237.90124.70723.19
112.91781.1183-1.8215.0835-1.32892.79190.07670.17260.1772-0.11130.12680.2533-0.0216-0.1272-0.20360.31570.00390.03980.41820.07080.28999.143-10.1764.589
121.7471.9542-2.12433.9078-2.22963.5504-0.04540.0689-0.1982-0.183-0.0848-0.23120.21070.00610.13020.2860.0098-0.01710.36780.04540.29146.657-22.212.748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 79
2X-RAY DIFFRACTION2A80 - 129
3X-RAY DIFFRACTION3B10 - 68
4X-RAY DIFFRACTION4B69 - 129
5X-RAY DIFFRACTION5C10 - 98
6X-RAY DIFFRACTION6C99 - 122
7X-RAY DIFFRACTION7D10 - 79
8X-RAY DIFFRACTION8D80 - 129
9X-RAY DIFFRACTION9E10 - 116
10X-RAY DIFFRACTION10E117 - 126
11X-RAY DIFFRACTION11F12 - 61
12X-RAY DIFFRACTION12F62 - 129

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