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- PDB-9gp5: Homodimer of BACH1 F9A mutant BTB domain -

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Basic information

Entry
Database: PDB / ID: 9gp5
TitleHomodimer of BACH1 F9A mutant BTB domain
ComponentsTranscription regulator protein BACH1
KeywordsDNA BINDING PROTEIN / BACH1 / back-to-back domain / BTB domain
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / ligand-modulated transcription factor activity / regulation of metabolic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / Regulation of BACH1 activity / Heme signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...Regulation of HMOX1 expression and activity / ligand-modulated transcription factor activity / regulation of metabolic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / Regulation of BACH1 activity / Heme signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / heme binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
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 / : / 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 ...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 / : / 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
Similarity search - Domain/homology
Transcription regulator protein BACH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchroeder, M. / Goretzki, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Bric-a-brac domain of BACH1 F9A mutant
Authors: Schroeder, M. / Goretzki, B.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Transcription regulator protein BACH1
D: Transcription regulator protein BACH1


Theoretical massNumber of molelcules
Total (without water)27,9642
Polymers27,9642
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-25 kcal/mol
Surface area11650 Å2
Unit cell
Length a, b, c (Å)31.084, 70.334, 65.246
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcription regulator protein BACH1 / BTB and CNC homolog 1 / HA2303


Mass: 13981.938 Da / Num. of mol.: 2 / Mutation: F9A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACH1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14867
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 51.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M HEPES, 0.15 M NaCl, 5% (w/v) glycerol, 0.001 M TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.9→70.33 Å / Num. obs: 22172 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Rrim(I) all: 0.092 / Χ2: 1.01 / Net I/σ(I): 11.4 / Num. measured all: 115094
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.63 / Num. measured all: 7737 / Num. unique obs: 1433 / CC1/2: 0.79 / Rpim(I) all: 0.292 / Rrim(I) all: 0.697 / Χ2: 1.05 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.573 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22555 1128 5.1 %RANDOM
Rwork0.19459 ---
obs0.19624 21023 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.237 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20.14 Å2
2--0.38 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.9→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 0 136 1891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161723
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.6332470
X-RAY DIFFRACTIONr_angle_other_deg0.5581.573960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.182510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62310311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
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_it2.3912.029931
X-RAY DIFFRACTIONr_mcbond_other2.3692.029931
X-RAY DIFFRACTIONr_mcangle_it3.4163.6221169
X-RAY DIFFRACTIONr_mcangle_other3.4153.6251170
X-RAY DIFFRACTIONr_scbond_it3.8372.444887
X-RAY DIFFRACTIONr_scbond_other3.8352.445888
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8144.2911302
X-RAY DIFFRACTIONr_long_range_B_refined7.7922.162077
X-RAY DIFFRACTIONr_long_range_B_other7.78722.032056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 72 -
Rwork0.246 1577 -
obs--99.88 %
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)
11.61611.5565-0.35454.0249-0.8191.2654-0.04-0.073-0.1275-0.0670.00670.07830.1598-0.18210.03330.0324-0.01160.00320.04830.00110.0288-3.9501-4.164417.8539
21.49531.27420.42063.49110.51021.2093-0.0848-0.09030.1186-0.02890.0298-0.1233-0.1790.11420.0550.0395-0.0012-0.01160.0378-0.00820.03334.010514.684917.892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C5 - 118
2X-RAY DIFFRACTION2D6 - 118

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