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- PDB-5xyw: Crystal structure of drosophila simulans Rhino chromoshadow domai... -

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Basic information

Entry
Database: PDB / ID: 5xyw
TitleCrystal structure of drosophila simulans Rhino chromoshadow domain in complex with N-terminal domain
Components
  • GD21652
  • Rhino
KeywordsPROTEIN BINDING / Chromoshadow / complex
Function / homology
Function and homology information


chromosome / nucleus
Similarity search - Function
: / : / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
Biological speciesDrosophila simulans (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.705 Å
AuthorsYu, B.W. / Huang, Y.
CitationJournal: EMBO Rep. / Year: 2018
Title: Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification
Authors: Yu, B. / Lin, Y.A. / Parhad, S.S. / Jin, Z. / Ma, J. / Theurkauf, W.E. / Zhang, Z.Z. / Huang, Y.
History
DepositionJul 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Rhino
B: Rhino
C: GD21652
D: GD21652


Theoretical massNumber of molelcules
Total (without water)29,1274
Polymers29,1274
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-39 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.893, 46.893, 250.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Rhino


Mass: 7569.646 Da / Num. of mol.: 2 / Fragment: UNP residues 440-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila simulans (fry) / Gene: rhi, Dsim\GD27086, Dsimw501_GD27086, GD25457 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q49BI5
#2: Protein GD21652


Mass: 6993.971 Da / Num. of mol.: 2 / Fragment: UNP residues 1-60
Source method: isolated from a genetically manipulated source
Details: In the electron density maps we only observed the main chain of 45Q, so we used Alanine instead.
Source: (gene. exp.) Drosophila simulans (fry) / Gene: Dsim\GD21652, Dsim_GD21652, GD21652 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4Q3Z0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.5 M NaCl, 0.1 M Tris (pH7.0), 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 14516 / % possible obs: 99.8 % / Redundancy: 21.4 % / Net I/σ(I): 39
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 14516 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.705→23.942 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.01
RfactorNum. reflection% reflection
Rfree0.3111 1465 10.09 %
Rwork0.2426 --
obs0.2494 14516 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.705→23.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 0 6 1445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011475
X-RAY DIFFRACTIONf_angle_d1.3391984
X-RAY DIFFRACTIONf_dihedral_angle_d15.453530
X-RAY DIFFRACTIONf_chiral_restr0.054211
X-RAY DIFFRACTIONf_plane_restr0.006240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7047-2.80120.37371470.33091252X-RAY DIFFRACTION95
2.8012-2.91320.33211490.29851327X-RAY DIFFRACTION100
2.9132-3.04550.3731440.28411278X-RAY DIFFRACTION100
3.0455-3.20570.31821480.27091312X-RAY DIFFRACTION100
3.2057-3.4060.38391470.26371317X-RAY DIFFRACTION100
3.406-3.66820.31521500.25041318X-RAY DIFFRACTION100
3.6682-4.03570.27731420.23131314X-RAY DIFFRACTION100
4.0357-4.61610.3031460.20261315X-RAY DIFFRACTION100
4.6161-5.80210.24721430.22141317X-RAY DIFFRACTION100
5.8021-23.94340.341490.25261301X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 23.0879 Å / Origin y: -6.7718 Å / Origin z: -19.5351 Å
111213212223313233
T0.4928 Å2-0.2042 Å2-0.0432 Å2-0.5815 Å2-0.001 Å2--0.4515 Å2
L1.0463 °2-0.576 °2-0.7101 °2-1.7877 °20.0794 °2--1.6218 °2
S0.0325 Å °-0.291 Å °0.1728 Å °-0.1174 Å °0.2702 Å °0.1536 Å °0.0642 Å °0.0837 Å °0.0032 Å °
Refinement TLS groupSelection details: all

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