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- PDB-6guw: BTB domain of zebrafish PATZ1 -

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Basic information

Entry
Database: PDB / ID: 6guw
TitleBTB domain of zebrafish PATZ1
ComponentsPOZ (BTB) and AT hook-containing zinc finger 1
KeywordsTRANSCRIPTION / Patz1 / BTB / zebrafish
Function / homology
Function and homology information


DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleoplasm
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
POZ/BTB and AT hook-containing zinc finger 1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAlt, A. / Piepoli, S. / Erman, B. / Mancini, E.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal SocietyNI140172 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2020
Title: Structural analysis of the PATZ1 BTB domain homodimer
Authors: Piepoli, S. / Alt, A. / Atilgan, C. / Mancini, E.J. / Erman, B.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POZ (BTB) and AT hook-containing zinc finger 1


Theoretical massNumber of molelcules
Total (without water)17,6971
Polymers17,6971
Non-polymers00
Water95553
1
A: POZ (BTB) and AT hook-containing zinc finger 1

A: POZ (BTB) and AT hook-containing zinc finger 1


Theoretical massNumber of molelcules
Total (without water)35,3942
Polymers35,3942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3510 Å2
ΔGint-27 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.080, 43.080, 123.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

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Components

#1: Protein POZ (BTB) and AT hook-containing zinc finger 1 / BTB domain


Mass: 17697.139 Da / Num. of mol.: 1 / Fragment: BTB domain, UNP residues 1-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: patz1 / Production host: Escherichia coli (E. coli) / References: UniProt: X1WGP9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.87 Å3/Da / Density % sol: 34.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 40% v/v PEG 500* MME; 20 % w/v PEG 20000; 0.1M Tris pH 8.5; 0.06M Magnesium chloride hexahydrate; 0.06 M Calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→41.22 Å / Num. obs: 12786 / % possible obs: 98.41 % / Redundancy: 2 % / Biso Wilson estimate: 36.06 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01302 / Rpim(I) all: 0.01302 / Net I/σ(I): 19.96
Reflection shellResolution: 1.8→1.865 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4871 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1120 / Χ2: 0.626 / % possible all: 87.99

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BUO

1buo


Resolution: 1.8→41.213 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.87
RfactorNum. reflection% reflection
Rfree0.2241 571 4.47 %
Rwork0.2152 --
obs0.2156 12785 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→41.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 0 53 993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007966
X-RAY DIFFRACTIONf_angle_d0.9651297
X-RAY DIFFRACTIONf_dihedral_angle_d4.116816
X-RAY DIFFRACTIONf_chiral_restr0.061145
X-RAY DIFFRACTIONf_plane_restr0.006164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8002-1.98140.31051240.29612844X-RAY DIFFRACTION94
1.9814-2.26810.26571230.24043073X-RAY DIFFRACTION100
2.2681-2.85740.2581610.24113061X-RAY DIFFRACTION100
2.8574-41.22410.20091630.19623236X-RAY DIFFRACTION100
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)
16.5356-4.3964-5.35815.84471.47615.95930.31990.09811.84140.40911.2622-2.4743-0.33112.6399-0.38320.4477-0.15760.07881.0233-0.32860.776633.246529.2125-9.2815
28.44231.1463-0.74147.73984.62645.50420.02621.13050.1528-0.3381-0.16240.401-0.2555-0.85130.15570.23850.08440.01150.4378-0.01880.21419.469626.7869-4.7344
32.67852.5872-0.9934.52822.60346.6219-0.10410.83770.0584-0.6989-0.31271.50590.0358-2.97140.66190.3245-0.23730.11370.9467-0.11270.6267-5.273221.67677.2321
43.958-2.60940.65833.51880.42131.7425-0.90490.3003-0.44641.274-0.29090.95220.8323-1.9414-0.41060.1041-0.02660.14190.6309-0.13840.31614.686722.94365.5166
53.47671.1893-1.38468.05931.09358.9718-0.465-0.121-1.15650.0411-0.3009-1.24491.03330.74411.06880.74050.08930.18810.41250.02040.42998.955618.622713.815
67.01830.2719-3.39275.94861.976.9913-0.17860.3003-0.63920.3657-0.29940.63020.5549-1.20550.23710.3077-0.00280.03210.5632-0.06170.41160.333126.39879.211
78.8112-0.4274-5.87256.71572.87556.34530.12860.51610.4440.58560.09930.3427-0.2297-0.8634-0.16680.37140.10540.03690.43320.02650.26262.745336.051515.3098
85.2817-3.9938-3.11035.0244.02424.17860.4525-0.21550.83970.3468-0.1586-2.2563-0.09561.1899-0.50580.51530.0241-0.00850.47720.01890.517810.533238.505718.0413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 60 )
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 99 )
7X-RAY DIFFRACTION7chain 'A' and (resid 100 through 119 )
8X-RAY DIFFRACTION8chain 'A' and (resid 120 through 135 )

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