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- PDB-8ru1: Chromatin remodeling regulator CECR2 with in crystallo disulfide bond -

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Basic information

Entry
Database: PDB / ID: 8ru1
TitleChromatin remodeling regulator CECR2 with in crystallo disulfide bond
ComponentsChromatin remodeling regulator CECR2
KeywordsTRANSCRIPTION / Crystal Epitopes / Bromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


CERF complex / neural fold formation / inner ear receptor cell stereocilium organization / cytoskeleton-dependent cytokinesis / apoptotic DNA fragmentation / ATP-dependent chromatin remodeler activity / execution phase of apoptosis / cochlea development / single fertilization / vesicle-mediated transport ...CERF complex / neural fold formation / inner ear receptor cell stereocilium organization / cytoskeleton-dependent cytokinesis / apoptotic DNA fragmentation / ATP-dependent chromatin remodeler activity / execution phase of apoptosis / cochlea development / single fertilization / vesicle-mediated transport / cytoskeleton organization / neural tube closure / euchromatin / chromatin remodeling / nucleus
Similarity search - Function
Chromatin remodeling regulator CECR2 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chromatin remodeling regulator CECR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Damerell, D. / Krojer, T. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionJan 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 2.0Mar 13, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry
Item: _entity.pdbx_number_of_molecules
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromatin remodeling regulator CECR2
B: Chromatin remodeling regulator CECR2
C: Chromatin remodeling regulator CECR2
D: Chromatin remodeling regulator CECR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,53616
Polymers54,9144
Non-polymers62112
Water6,395355
1
A: Chromatin remodeling regulator CECR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9136
Polymers13,7291
Non-polymers1845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chromatin remodeling regulator CECR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8443
Polymers13,7291
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chromatin remodeling regulator CECR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8443
Polymers13,7291
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chromatin remodeling regulator CECR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9364
Polymers13,7291
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.910, 77.200, 78.140
Angle α, β, γ (deg.)90.000, 91.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Chromatin remodeling regulator CECR2 / Cat eye syndrome critical region protein 2


Mass: 13728.618 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CECR2, KIAA1740 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXF3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3M sodium chloride 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.66→46.93 Å / Num. obs: 61333 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 18.2
Reflection shellResolution: 1.66→1.7 Å / Num. unique obs: 4508 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→46.93 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.09
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2103 2939 4.792 %
Rwork0.1832 58394 -
all0.185 --
obs-61333 99.45 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.695 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å2-0 Å20.127 Å2
2--2.546 Å20 Å2
3---0.188 Å2
Refinement stepCycle: LAST / Resolution: 1.66→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 37 364 3706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123438
X-RAY DIFFRACTIONr_bond_other_d0.0250.0163128
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.8464628
X-RAY DIFFRACTIONr_angle_other_deg1.9111.7977141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7935416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.61515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70410592
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.0261012
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.92210164
X-RAY DIFFRACTIONr_chiral_restr0.0580.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023968
X-RAY DIFFRACTIONr_gen_planes_other00.02812
X-RAY DIFFRACTIONr_nbd_refined0.2160.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22954
X-RAY DIFFRACTIONr_nbtor_refined0.1970.21720
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1010.21746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.222
X-RAY DIFFRACTIONr_nbd_other0.190.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4170.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0230.21
X-RAY DIFFRACTIONr_mcbond_it3.4713.2561649
X-RAY DIFFRACTIONr_mcbond_other3.4793.2561649
X-RAY DIFFRACTIONr_mcangle_it4.2745.8212058
X-RAY DIFFRACTIONr_mcangle_other4.2775.8222059
X-RAY DIFFRACTIONr_scbond_it5.2783.6591789
X-RAY DIFFRACTIONr_scbond_other5.2823.661790
X-RAY DIFFRACTIONr_scangle_it6.9856.5272566
X-RAY DIFFRACTIONr_scangle_other6.9846.5282567
X-RAY DIFFRACTIONr_lrange_it7.21236.0454195
X-RAY DIFFRACTIONr_lrange_other7.21935.7894116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.66-1.7030.2791910.27743150.27845250.9130.91999.58010.247
1.703-1.750.2672070.2642030.2644180.9360.93299.81890.223
1.75-1.80.2732050.23640960.23843080.9340.94699.83750.2
1.8-1.8560.2471910.22839710.22941760.9540.95499.66480.193
1.856-1.9160.2672140.21137910.21440190.950.96499.65160.18
1.916-1.9840.2341550.20737770.20839410.9640.96799.77160.175
1.984-2.0580.2431740.19336150.19637950.9590.97299.84190.166
2.058-2.1420.21810.18434730.18536590.9750.97699.86330.162
2.142-2.2370.2041820.17633190.17835050.9730.97999.88590.158
2.237-2.3460.221540.1831730.18233350.9660.97899.76010.167
2.346-2.4730.1981720.17629950.17731750.9760.97999.7480.166
2.473-2.6220.251410.18728630.18930110.9630.97799.76750.178
2.622-2.8030.2331300.18327040.18528500.9650.97799.43860.18
2.803-3.0260.1861130.17825150.17926390.9760.97999.58320.183
3.026-3.3140.2061230.18522840.18624300.9750.97999.05350.194
3.314-3.7030.1771100.16420770.16522180.9840.98498.60230.178
3.703-4.2710.196840.14518240.14719520.9750.98797.74590.166
4.271-5.220.1951060.15815160.16116660.9770.98597.35890.189
5.22-7.3370.242550.22512210.22613020.9670.97398.00310.26
7.337-46.930.188510.1976620.1967460.9740.97595.57640.243

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