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- PDB-4quc: Crystal structure of chromodomain of Rhino -

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Basic information

Entry
Database: PDB / ID: 4quc
TitleCrystal structure of chromodomain of Rhino
ComponentsRE36324p
KeywordsPROTEIN BINDING / histone binding
Function / homology
Function and homology information


piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / piRNA processing / chromosome organization / heterochromatin / pericentric heterochromatin / methylated histone binding ...piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / piRNA processing / chromosome organization / heterochromatin / pericentric heterochromatin / methylated histone binding / transcription antitermination / heterochromatin formation / chromatin binding / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / : / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...: / : / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromo domain-containing protein rhino
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsLi, S. / Patel, D.J.
CitationJournal: Genes Dev. / Year: 2014
Title: Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing.
Authors: Le Thomas, A. / Stuwe, E. / Li, S. / Du, J. / Marinov, G. / Rozhkov, N. / Chen, Y.C. / Luo, Y. / Sachidanandam, R. / Toth, K.F. / Patel, D. / Aravin, A.A.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RE36324p


Theoretical massNumber of molelcules
Total (without water)7,8861
Polymers7,8861
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.480, 36.480, 76.115
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

21A-126-

HOH

31A-129-

HOH

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Components

#1: Protein RE36324p / Rhino


Mass: 7885.945 Da / Num. of mol.: 1 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG10683, Dmel_CG10683, rhi, rhino / Plasmid: pETsumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q7JXA8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.85 Å3/Da / Density % sol: 33.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Sodium nitrate and 20%(w/v) PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.029 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.029 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 9886 / Num. obs: 9293 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 61.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 3.1 / Num. unique all: 811 / Rsym value: 0.653 / % possible all: 85

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KNE

1kne


Resolution: 1.502→14.589 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 441 4.76 %RANDOM
Rwork0.2112 ---
all0.2131 9706 --
obs0.2131 9265 94.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.502→14.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms461 0 0 45 506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01472
X-RAY DIFFRACTIONf_angle_d1.252638
X-RAY DIFFRACTIONf_dihedral_angle_d13.451176
X-RAY DIFFRACTIONf_chiral_restr0.0867
X-RAY DIFFRACTIONf_plane_restr0.00583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5023-1.71940.33131380.24392769X-RAY DIFFRACTION91
1.7194-2.16510.27731570.24962979X-RAY DIFFRACTION97
2.1651-14.59020.23871460.19963076X-RAY DIFFRACTION95
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)
12.9308-2.66851.567.91932.03982.98870.22530.5688-0.0844-0.1837-0.18380.2365-0.5466-0.46590.00140.40390.0945-0.03680.3222-0.00520.226-18.476.365612.5135
26.9603-2.21213.71754.1988-2.83725.5917-0.1568-0.30940.26820.2310.1242-0.2735-0.0496-0.49440.07220.25610.01520.00030.2792-0.06520.232-13.1573.539317.789
32.1529-1.7594-0.82316.51721.60326.8017-0.02520.4273-0.1821-0.48690.2266-0.643-0.36220.3781-0.13720.4070.00480.04740.332-0.1150.3384-7.887467.96535.866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 78 )

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