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- PDB-5ptv: PanDDA analysis group deposition -- Crystal Structure of BRD1 aft... -

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Basic information

Entry
Database: PDB / ID: 5ptv
TitlePanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 173)
ComponentsBromodomain-containing protein 1
KeywordsGENE REGULATION / PanDDA / SGC - Diamond I04-1 fragment screening / bromodomain / epigenetics / XChemExplorer
Function / homology
Function and homology information


histone H3-K14 acetyltransferase complex / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / histone reader activity / positive regulation of erythrocyte differentiation ...histone H3-K14 acetyltransferase complex / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / histone reader activity / positive regulation of erythrocyte differentiation / HATs acetylate histones / histone binding / perikaryon / nuclear speck / chromatin remodeling / dendrite / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
BRPF2, ePHD domain / BRPF2, PHD domain / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif ...BRPF2, ePHD domain / BRPF2, PHD domain / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.7 Å
AuthorsPearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. ...Pearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Renjie, Z. / Dias, A. / Ng, J. / Brennan, P.E. / Cox, O. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: Nat Commun / Year: 2017
Title: A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Authors: Pearce, N.M. / Krojer, T. / Bradley, A.R. / Collins, P. / Nowak, R.P. / Talon, R. / Marsden, B.D. / Kelm, S. / Shi, J. / Deane, C.M. / von Delft, F.
History
DepositionFeb 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_deposit_group
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_deposit_group.group_title / _pdbx_deposit_group.group_type
Revision 1.2Oct 4, 2017Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_title
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 1
B: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7217
Polymers36,4492
Non-polymers2715
Water4,666259
1
A: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3493
Polymers18,2251
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3724
Polymers18,2251
Non-polymers1473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.535, 56.506, 101.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 1 / BR140-like protein / Bromodomain and PHD finger-containing protein 2


Mass: 18224.680 Da / Num. of mol.: 2 / Mutation: V23M,P34E,V37R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1, BRL, BRPF2 / Production host: Escherichia coli (E. coli) / References: UniProt: O95696
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.19 Å3/Da / Density % sol: 43.92 % / Mosaicity: 0.07 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M bis-tris pH 7.0 -- 30% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→29.11 Å / Num. obs: 36097 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Net I/σ(I): 17.3 / Num. measured all: 240605 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.746.80.971723225520.7420.4011.0512.197.5
7.59-29.116.20.02329574790.9990.010.02565.298.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0131refinement
Aimless0.3.6data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5AMF

5amf


Resolution: 1.7→29.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.273 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1739 4.8 %RANDOM
Rwork0.1851 ---
obs0.1867 34304 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.58 Å2 / Biso mean: 24.056 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å2-0 Å20 Å2
2---1.02 Å2-0 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 1.7→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 21 259 2233
Biso mean--34.37 31.49 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192083
X-RAY DIFFRACTIONr_bond_other_d0.0030.022008
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9752815
X-RAY DIFFRACTIONr_angle_other_deg1.08334599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7125264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63723.509114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38615380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1811525
X-RAY DIFFRACTIONr_chiral_restr0.1160.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
X-RAY DIFFRACTIONr_mcbond_it2.2572.2091002
X-RAY DIFFRACTIONr_mcbond_other2.2292.2051001
X-RAY DIFFRACTIONr_mcangle_it3.0513.2911257
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 141 -
Rwork0.307 2405 -
all-2546 -
obs--97.25 %

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