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- PDB-7po9: Crystal structure of ZAD-domain of M1BP protein from D.melanogaster -

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Basic information

Entry
Database: PDB / ID: 7po9
TitleCrystal structure of ZAD-domain of M1BP protein from D.melanogaster
ComponentsLD30467p
KeywordsTRANSCRIPTION / Zinc-finger associated domain / ZAD / protein interaction / dimerization / M1BP / 9797 / zinc binding / treble-cleft-like
Function / homology
Function and homology information


follicle cell of egg chamber development / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / positive regulation of ERK1 and ERK2 cascade / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / 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: 1.9 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 8, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LD30467p
B: LD30467p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1914
Polymers22,0602
Non-polymers1312
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-31 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.853, 48.827, 141.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 12 - 94 / Label seq-ID: 11 - 93

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein LD30467p / Motif 1 binding protein


Mass: 11029.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: M1BP, CC31, Dmel\CG9797, CG9797, Dmel_CG9797 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VHM3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M Calcium Acetate, 0.1MES pH 6.0, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→141.59 Å / Num. obs: 21730 / % possible obs: 97.9 % / Redundancy: 11.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.018 / Rrim(I) all: 0.061 / Net I/σ(I): 13.6 / Num. measured all: 250275
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
1.7-1.736.82.27562489190.6770.9292.470.280.6
9-141.599.60.03219572040.9990.0110.034114.699.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
Aimless0.7.7data scaling
SHELXDEphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.9→70.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2609 / WRfactor Rwork: 0.2122 / FOM work R set: 0.5885 / SU B: 9.014 / SU ML: 0.228 / SU R Cruickshank DPI: 0.1718 / SU Rfree: 0.1641 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2863 771 4.8 %RANDOM
Rwork0.2411 ---
obs0.2434 15232 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.36 Å2 / Biso mean: 61.59 Å2 / Biso min: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.37 Å2-0 Å2-0 Å2
2--0.62 Å2-0 Å2
3---3.75 Å2
Refinement stepCycle: final / Resolution: 1.9→70.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 2 11 1331
Biso mean--53.57 50.74 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131346
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171308
X-RAY DIFFRACTIONr_angle_refined_deg2.0951.6631803
X-RAY DIFFRACTIONr_angle_other_deg1.4061.5833009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97820.65876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.42615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.761516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021506
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02306
Refine LS restraints NCS

Ens-ID: 1 / Number: 2145 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.19 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 61 -
Rwork0.438 1101 -
all-1162 -
obs--100 %

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