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- PDB-7poh: Crystal structure of ZAD-domain of Serendipity-d protein from D.m... -

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Basic information

Entry
Database: PDB / ID: 7poh
TitleCrystal structure of ZAD-domain of Serendipity-d protein from D.melanogaster
ComponentsSerendipity locus protein delta
KeywordsTRANSCRIPTION / Zinc-finger associated domain / ZAD / protein interaction / dimerization / Serenipity-d / zinc binding / treble-cleft-like
Function / homology
Function and homology information


polytene chromosome interband / bicoid mRNA localization / anterior/posterior axis specification, embryo / sexual reproduction / oogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II ...polytene chromosome interband / bicoid mRNA localization / anterior/posterior axis specification, embryo / sexual reproduction / oogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytosol
Similarity search - Function
: / Zinc-finger of C2H2 type / 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
Serendipity locus protein delta
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsBoyko, K.M. / Kachalova, G.S. / 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
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serendipity locus protein delta
B: Serendipity locus protein delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7126
Polymers21,4512
Non-polymers2624
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-70 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.161, 99.161, 117.667
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serendipity locus protein delta


Mass: 10725.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sry-delta, Sry-d, CG17958 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07664
#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


Mass: 18.015 Da / Num. of mol.: 4 / 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

Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1.3M Lithium sulfate 1.3M, 0.1M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.85→99.16 Å / Num. obs: 12833 / % possible obs: 91.3 % / Redundancy: 4.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.045 / Rrim(I) all: 0.1 / Net I/σ(I): 9 / Num. measured all: 57927
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.85-34.70.85318740.6490.4310.96192.9
9.01-99.164.20.0464440.990.0250.05386.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
HKL-2000data reduction
Aimless0.7.7data scaling
SHELXphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.85→70.12 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2273 / WRfactor Rwork: 0.1998 / FOM work R set: 0.6919 / SU B: 25.099 / SU ML: 0.219 / SU R Cruickshank DPI: 0.2983 / SU Rfree: 0.2434 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 633 4.9 %RANDOM
Rwork0.2176 ---
obs0.2187 12183 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 192.27 Å2 / Biso mean: 79.734 Å2 / Biso min: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å2-0 Å2-0 Å2
2--0.96 Å2-0 Å2
3----1.93 Å2
Refinement stepCycle: final / Resolution: 2.85→70.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 4 4 1384
Biso mean--99.2 60.53 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131401
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171329
X-RAY DIFFRACTIONr_angle_refined_deg2.5421.6671893
X-RAY DIFFRACTIONr_angle_other_deg1.4271.5773065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4455176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.63823.27961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.67215249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.888157
X-RAY DIFFRACTIONr_chiral_restr0.1220.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021534
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02292
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 40 -
Rwork0.443 916 -
all-956 -
obs--92.01 %
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)
11.191-0.947-1.06494.6304-1.56752.5092-0.1285-0.20820.11540.5750.2006-0.0505-0.11640.1006-0.07220.1326-0.04480.01830.1257-0.07010.109223.46840.134564.9007
23.3659-1.631.81374.0463-3.90374.610.13930.1778-0.1171-0.7680.30.36130.8267-0.2861-0.43930.2047-0.0632-0.09580.06490.02040.063813.975645.287540.9698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 93
2X-RAY DIFFRACTION2B-2 - 92

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