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- PDB-5cqq: Crystal structure of the Drosophila Zeste DNA binding domain in c... -

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Basic information

Entry
Database: PDB / ID: 5cqq
TitleCrystal structure of the Drosophila Zeste DNA binding domain in complex with DNA
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*CP*GP*AP*GP*TP*GP*GP*AP*AP*AP*AP*CP*AP*G)-3')
  • DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3')
  • Regulatory protein zeste
KeywordsTRANSCRIPTION/DNA / Complex / Protein-DNA interaction / Tanscription factor / Gene regulation / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


ommochrome biosynthetic process / : / polytene chromosome interband / PRC1 complex / sequence-specific DNA binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / nucleus
Similarity search - Function
Myb/SANT-like DNA-binding domain 5 / Myb/SANT-like DNA-binding domain
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein zeste
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsGao, G.N. / Wang, M. / Yang, N. / Huang, Y. / Xu, R.M.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31430018 China
National Natural Science Foundation of China31210103914 China
National Natural Science Foundation of China31470719 China
MOST2015CB856202 China
CASXDB08010100 China
CASKJZDEW-L05 China
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure of Zeste-DNA Complex Reveals a New Modality of DNA Recognition by Homeodomain-Like Proteins
Authors: Gao, G.N. / Wang, M. / Yang, N. / Huang, Y. / Xu, R.M.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein zeste
B: Regulatory protein zeste
C: DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(*AP*AP*AP*AP*AP*CP*GP*AP*GP*TP*GP*GP*AP*AP*AP*AP*CP*AP*G)-3')
E: DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3')
F: DNA (5'-D(*AP*AP*AP*AP*AP*CP*GP*AP*GP*TP*GP*GP*AP*AP*AP*AP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)43,5006
Polymers43,5006
Non-polymers00
Water362
1
A: Regulatory protein zeste
C: DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(*AP*AP*AP*AP*AP*CP*GP*AP*GP*TP*GP*GP*AP*AP*AP*AP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)21,7503
Polymers21,7503
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-20 kcal/mol
Surface area10620 Å2
MethodPISA
2
B: Regulatory protein zeste
E: DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3')
F: DNA (5'-D(*AP*AP*AP*AP*AP*CP*GP*AP*GP*TP*GP*GP*AP*AP*AP*AP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)21,7503
Polymers21,7503
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-17 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.007, 59.705, 202.160
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
11chain A
21chain B
12chain C
22chain E
13chain D
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTYRTYRchain AAA52 - 1304 - 82
21LEULEUTYRTYRchain BBB52 - 1304 - 82
12DCDCDTDTchain CCC1 - 191 - 19
22DCDCDTDTchain EEE1 - 191 - 19
13DADADGDGchain DDD1 - 191 - 19
23DADADGDGchain FFF1 - 191 - 19

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Regulatory protein zeste


Mass: 10102.642 Da / Num. of mol.: 2 / Fragment: UNP residues 51-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: z, CG7803 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09956
#2: DNA chain DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*CP*CP*AP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3')


Mass: 5718.691 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: DNA chain DNA (5'-D(*AP*AP*AP*AP*AP*CP*GP*AP*GP*TP*GP*GP*AP*AP*AP*AP*CP*AP*G)-3')


Mass: 5928.903 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.54 Å3/Da / Density % sol: 65.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 10 mM sodium citrate, pH 4.2, 24% PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 27.2 % / Number: 337678 / Rsym value: 0.144 / D res high: 3.1 Å / D res low: 46.675 Å / Num. obs: 12435 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
9.846.6710.0780.07821.3
6.939.810.0790.07924
5.666.9310.150.1525.9
4.95.6610.140.1426.8
4.384.910.1290.12927.3
44.3810.1690.16927.5
3.71410.2310.23127.9
3.473.7110.3080.30827.9
3.273.4710.3470.34728.2
3.13.2710.420.4228.3
ReflectionResolution: 3.1→50 Å / Num. all: 12435 / Num. obs: 12079 / % possible obs: 98.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 71.28 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Rrim(I) all: 0.15 / Rsym value: 0.144 / Χ2: 1.154 / Net I/av σ(I): 18.669 / Net I/σ(I): 10.6 / Num. measured all: 69974
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueΧ2Net I/σ(I) obs% possible all
3.1-3.2160.4016.14982812340.0810.421.0745.5100
3.21-3.3460.231.74725711480.0670.3471.1747.499.7
3.34-3.4960.2082.14426011980.060.3081.1629.3100
3.49-3.6860.172.54174112030.0460.2311.18912.3100
3.68-3.9160.1323.73795111840.0330.1691.27715.899.8
3.91-4.215.90.114.73358412160.0260.1291.20319.899.5
4.21-4.635.90.0924.12996612160.0280.141.17321.899.3
4.63-5.35.80.0933.92493512130.030.151.19125.199.3
5.3-6.675.60.0856.41838012450.0170.0791.10630.699.4
6.67-504.90.047.5977612220.0190.0780.96130.890.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→49.457 Å / FOM work R set: 0.7502 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 553 4.8 %Random selection
Rwork0.2223 10962 --
obs0.224 11515 97.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.72 Å2 / Biso mean: 88.97 Å2 / Biso min: 55.42 Å2
Refinement stepCycle: final / Resolution: 3.1→49.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 1546 0 2 2860
Biso mean---73.96 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053080
X-RAY DIFFRACTIONf_angle_d1.0494481
X-RAY DIFFRACTIONf_chiral_restr0.04489
X-RAY DIFFRACTIONf_plane_restr0.004302
X-RAY DIFFRACTIONf_dihedral_angle_d25.0481257
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A716X-RAY DIFFRACTION7.302TORSIONAL
12B716X-RAY DIFFRACTION7.302TORSIONAL
21C372X-RAY DIFFRACTION7.302TORSIONAL
22E372X-RAY DIFFRACTION7.302TORSIONAL
31D372X-RAY DIFFRACTION7.302TORSIONAL
32F372X-RAY DIFFRACTION7.302TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.41190.2761470.24512647279496
3.4119-3.90550.27151340.2592711284598
3.9055-4.91980.28171430.24632775291899
4.9198-49.46330.24041290.19362829295896

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