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- PDB-3nxb: Crystal Structure of the Bromodomain of human CECR2 -

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Basic information

Entry
Database: PDB / ID: 3nxb
TitleCrystal Structure of the Bromodomain of human CECR2
ComponentsCat eye syndrome critical region protein 2
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC / CECR2 / cat eye syndrome chromosome region candidate 2 / bromodomain / structural genomics
Function / homology
Function and homology information


neural fold formation / CERF complex / inner ear receptor cell stereocilium organization / apoptotic DNA fragmentation / cytoskeleton-dependent cytokinesis / ATP-dependent chromatin remodeler activity / execution phase of apoptosis / cochlea development / single fertilization / vesicle-mediated transport ...neural fold formation / CERF complex / inner ear receptor cell stereocilium organization / apoptotic DNA fragmentation / cytoskeleton-dependent cytokinesis / 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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily ...Chromatin remodeling regulator CECR2 / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chromatin remodeling regulator CECR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cat eye syndrome critical region protein 2
B: Cat eye syndrome critical region protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9005
Polymers27,7142
Non-polymers1863
Water3,765209
1
A: Cat eye syndrome critical region protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9192
Polymers13,8571
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cat eye syndrome critical region protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9813
Polymers13,8571
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.160, 45.510, 45.590
Angle α, β, γ (deg.)90.000, 105.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cat eye syndrome critical region protein 2


Mass: 13856.856 Da / Num. of mol.: 2 / Fragment: BROMODOMAIN (unp residues 424-538)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CECR2, KIAA1740 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9BXF3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 12% PEG 20,000, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 9.1 / Number: 77360 / Rsym value: 0.058 / D res high: 1.825 Å / D res low: 22.919 Å / Num. obs: 22346 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.7722.9298.410.0330.0333.4
4.085.7710010.0340.0343.5
3.334.0810010.0390.0393.5
2.893.3310010.0470.0473.5
2.582.8910010.0580.0583.5
2.362.5899.610.0820.0823.5
2.182.3699.610.1290.1293.5
2.042.1898.710.1980.1983.4
1.922.0498.810.3520.3523.4
1.831.9298.410.5410.5413.4
ReflectionResolution: 1.83→29.25 Å / Num. all: 22503 / Num. obs: 22346 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.83-1.923.40.5411.41077331810.54198.4
1.92-2.043.40.3522.21044830560.35298.8
2.04-2.183.40.1983.6990228810.19898.7
2.18-2.363.50.1295.4924626760.12999.6
2.36-2.583.50.0829.1875425020.08299.6
2.58-2.893.50.05812.2789722550.058100
2.89-3.333.50.04713.4709120100.047100
3.33-4.083.50.03916603617130.039100
4.08-5.773.50.03416.8469813280.034100
5.77-22.9193.40.03316.225157440.03398.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.9 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.92 Å
Translation2.5 Å22.92 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

2oss

2ouo

2grc

2oo1

3dai

3d7c

3dwy


Resolution: 1.83→29.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.1689 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8603 / SU B: 5.461 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1225 / SU Rfree: 0.1189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 1147 5.1 %RANDOM
Rwork0.1764 ---
all0.1784 22501 --
obs0.1784 22343 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.22 Å2 / Biso mean: 29.5597 Å2 / Biso min: 13.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.26 Å2
2--0.06 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.83→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 12 209 1860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221720
X-RAY DIFFRACTIONr_bond_other_d0.0010.021235
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9632298
X-RAY DIFFRACTIONr_angle_other_deg0.90533002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68924.21783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49715329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.07159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
LS refinement shellResolution: 1.83→1.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.539 66 -
Rwork0.448 1520 -
all-1586 -
obs--98.69 %
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)
10.8978-0.11180.04080.59760.15080.6448-0.0079-0.02750.0266-0.01820.06580.06640.0950.0512-0.0580.07560.0233-0.00210.05560.02440.050424.61215.238116.7843
21.46370.4080.02780.79430.5730.47850.0206-0.0197-0.2992-0.0827-0.0351-0.0544-0.0953-0.01330.01450.0667-0.0131-0.00370.05390.03860.109812.587221.01191.0261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A437 - 537
2X-RAY DIFFRACTION2B438 - 537

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