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- PDB-3ohv: Crystal structure of the human Bach2 POZ domain, form II -

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Basic information

Entry
Database: PDB / ID: 3ohv
TitleCrystal structure of the human Bach2 POZ domain, form II
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 / Basic-leucine zipper domain superfamily ...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 superfamily / Basic-leucine zipper domain / 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: 2.2 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
Water3,891216
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 area4380 Å2
ΔGint-42 kcal/mol
Surface area12890 Å2
MethodPISA
2
C: Transcription regulator protein BACH2
D: 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 area3830 Å2
ΔGint-35 kcal/mol
Surface area12340 Å2
MethodPISA
3
E: 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 area4190 Å2
ΔGint-38 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.680, 96.950, 82.480
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.: 216 / 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: 51.8 %
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: Feb 5, 2010 / 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: 2.2→48.48 Å / Num. all: 43663 / Num. obs: 43314 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 33.012 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.126 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6332 / Rsym value: 0.865 / % 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 code 3ohu

3ohu


Resolution: 2.2→48.48 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.897 / SU B: 16.404 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27349 2180 5 %RANDOM
Rwork0.22348 ---
all0.22348 41482 --
obs0.22608 41113 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.725 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å20 Å22.23 Å2
2---2.29 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5731 0 0 216 5947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225949
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9618075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17823.297276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.336151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7261549
X-RAY DIFFRACTIONr_chiral_restr0.0870.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024457
X-RAY DIFFRACTIONr_mcbond_it0.5661.53660
X-RAY DIFFRACTIONr_mcangle_it1.05625910
X-RAY DIFFRACTIONr_scbond_it1.58932289
X-RAY DIFFRACTIONr_scangle_it2.5394.52160
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 157 -
Rwork0.337 3000 -
obs--99.68 %
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)
10.26260.3312-0.1722.4671.04030.9170.01180.04280.002-0.037-0.02860.0911-0.0465-0.02280.01680.13270.0154-0.05550.20180.02690.184926.7491.3615.806
21.02230.0753-1.20721.83870.03463.42680.1269-0.08530.05150.2682-0.06180.19590.0051-0.0054-0.06510.101-0.0239-0.01740.17490.04110.154221.4565.1222.071
31.09860.2917-0.81571.40220.85444.7258-0.13760.0221-0.0207-0.2487-0.11450.0558-0.0538-0.05390.25210.1809-0.0017-0.0650.07150.01780.167724.453-3.8682.145
41.75121.57020.32553.4280.25151.3831-0.06690.14950.0149-0.0913-0.0134-0.1366-0.26030.21690.08020.1697-0.0081-0.01960.15520.00840.131230.832-13.95-7.336
51.75-0.1087-0.87131.5568-0.50151.86010.0414-0.01740.0465-0.03380.0181-0.0862-0.07660.0747-0.05950.138-0.0031-0.02170.1513-0.02990.20311.47321.2982.348
60.82240.2762-0.2992.0087-0.17291.2362-0.10950.0405-0.29040.28570.01920.02580.2450.01040.09030.15840.0123-0.02250.1181-0.01970.2467-0.7236.287.701
71.09350.2456-0.00022.54-0.93251.1163-0.03450.04620.123-0.26770.0462-0.0754-0.00230.0445-0.01180.1344-0.013-0.01940.1628-0.03630.1643.94728.745-11.126
818.09789.007-12.7144.74-4.703321.5044-1.2681.3099-0.2491-0.49740.7378-0.07311.78180.16170.53010.29090.01260.19170.24110.05150.17616.39724.942-18.06
92.76630.5312-0.80723.57540.12332.15170.07580.03720.1377-0.023-0.03460.16110.0018-0.1772-0.04110.1484-0.00020.06390.22340.08790.102817.06-9.417-35.787
101.43241.2656-1.3712.7792-1.11942.1867-0.07560.1945-0.0925-0.2047-0.0795-0.25140.22730.02550.15520.12770.00310.00530.20410.05270.13215.642-21.506-29.253
111.69851.1119-1.79811.8451-1.5032.75390.14920.02820.10480.10920.02020.1477-0.14650.0262-0.16940.16640.01530.04680.18370.03460.119924.463-0.751-37.427
124.32993.7537-1.32564.83143.675618.97140.7416-0.29691.23910.3626-0.43170.8771-1.2379-0.2332-0.30990.4130.09030.35970.1130.04330.585620.26714.837-34.809
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 78
2X-RAY DIFFRACTION2A79 - 129
3X-RAY DIFFRACTION3B9 - 59
4X-RAY DIFFRACTION4B60 - 129
5X-RAY DIFFRACTION5C11 - 76
6X-RAY DIFFRACTION6C77 - 129
7X-RAY DIFFRACTION7D10 - 116
8X-RAY DIFFRACTION8D117 - 126
9X-RAY DIFFRACTION9E11 - 61
10X-RAY DIFFRACTION10E62 - 129
11X-RAY DIFFRACTION11F10 - 97
12X-RAY DIFFRACTION12F98 - 126

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