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- PDB-7pok: Crystal structure of ZAD-domain of Pita protein from D.melanogaster -

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Basic information

Entry
Database: PDB / ID: 7pok
TitleCrystal structure of ZAD-domain of Pita protein from D.melanogaster
ComponentsLD15650p
KeywordsTRANSCRIPTION / Zinc-finger associated domain / ZAD / protein interaction / dimerization / Pita / insulator / zinc binding / treble-cleft-like
Function / homology
Function and homology information


: / DNA endoreduplication / chromatin insulator sequence binding / polytene chromosome / DNA replication / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription ...: / DNA endoreduplication / chromatin insulator sequence binding / polytene chromosome / DNA replication / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
ZAD domain profile. / Zinc-finger associated domain (zf-AD) / Zinc finger, AD-type / Zinc-finger associated domain (zf-AD) / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBoyko, K.M. / Bonchuk, A.N. / Nikolaeva, A.Y. / Georgiev, P.G. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-10099 Russian Federation
CitationJournal: Structure / Year: 2022
Title: Structural insights into highly similar spatial organization of zinc-finger associated domains with a very low sequence similarity.
Authors: Bonchuk, A.N. / Boyko, K.M. / Nikolaeva, A.Y. / Burtseva, A.D. / Popov, V.O. / Georgiev, P.G.
History
DepositionSep 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LD15650p
B: LD15650p
C: LD15650p
D: LD15650p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5818
Polymers54,3204
Non-polymers2624
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-121 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.265, 90.489, 105.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 108
2010B15 - 108
1020A15 - 111
2020C15 - 111
1030A15 - 109
2030D15 - 109
1040B14 - 108
2040C14 - 108
1050B15 - 108
2050D15 - 108
1060C15 - 109
2060D15 - 109

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
LD15650p / Pita / isoform A


Mass: 13579.909 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: pita, Dmel\CG3941, PITA, Pita, spdk, CG3941, Dmel_CG3941
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q95RQ8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 20% PEG 10 000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→105.77 Å / Num. obs: 38834 / % possible obs: 99.4 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 14 / Num. measured all: 240385
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8461.1951355222620.730.5251.3080.598.9
9-105.775.70.02720963660.9990.0120.0385.499.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
CRANK22.0.281phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→62.81 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.893 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1941 5 %RANDOM
Rwork0.1897 ---
obs0.1913 36863 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.85 Å2 / Biso mean: 45.148 Å2 / Biso min: 23.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2---1.28 Å20 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.8→62.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 4 167 3099
Biso mean--39.24 47.45 -
Num. residues----371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133058
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172960
X-RAY DIFFRACTIONr_angle_refined_deg2.0951.6724131
X-RAY DIFFRACTIONr_angle_other_deg1.4331.5716839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1615368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66720.263152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30915548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3351527
X-RAY DIFFRACTIONr_chiral_restr0.1050.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A25230.13
12B25230.13
21A25640.12
22C25640.12
31A25630.14
32D25630.14
41B25050.12
42C25050.12
51B25510.12
52D25510.12
61C24930.12
62D24930.12
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 139 -
Rwork0.369 2689 -
all-2828 -
obs--98.54 %
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)
10.9811-0.33460.09081.68620.42311.23020.10870.06320.05850.04330.1098-0.242-0.07470.1109-0.21850.11920.00130.01550.0196-0.02490.058437.240620.154617.5775
20.69590.46750.95413.27772.09432.78240.0741-0.02460.05140.0207-0.13780.431-0.0696-0.33470.06370.10010.03050.04460.08810.04430.11212.946822.961619.0419
30.53090.79130.54223.1011.87872.6750.127-0.0316-0.10720.5643-0.00180.0660.3238-0.1593-0.12530.2196-0.01310.03430.02270.02880.073218.60915.927228.2617
40.40870.0582-0.25364.07261.25021.2630.04780.14520.0832-0.3080.02520.0303-0.2231-0.0887-0.0730.14970.01730.00230.05160.02950.020728.530824.3047.887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 112
2X-RAY DIFFRACTION2B11 - 109
3X-RAY DIFFRACTION3C14 - 111
4X-RAY DIFFRACTION4D15 - 109

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