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- PDB-5poj: PanDDA analysis group deposition -- Crystal Structure of BRD1 in ... -

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Basic information

Entry
Database: PDB / ID: 5poj
TitlePanDDA analysis group deposition -- Crystal Structure of BRD1 in complex with N10941a
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 / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / 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 / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / 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 / metal ion binding / nucleus
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 / PWWP domain ...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
N-(1-benzylpiperidin-4-yl)acetamide / Bromodomain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.62 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 15, 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)37,1238
Polymers36,4492
Non-polymers6746
Water4,846269
1
A: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5814
Polymers18,2251
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5424
Polymers18,2251
Non-polymers3173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.716, 56.384, 101.685
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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-8RV / N-(1-benzylpiperidin-4-yl)acetamide


Mass: 232.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N2O
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details yes CC(NC1CCN(CC1)Cc1ccccc1)=O None -9.52 13.01 13.01 CC(NC1CCN(CC1)Cc1ccccc1)=O 4 - High ... yes CC(NC1CCN(CC1)Cc1ccccc1)=O -9.52 13.01 13.01 CC(NC1CCN(CC1)Cc1ccccc1)=O 4 - High Confidence None 0.63 19.47705882352941 1.0291461574542393 0.91200000000000003 0.10000000000000001 1.8 0.22446170903637305 -30.33 4.73 4.73 CC(NC1CCN(CC1)Cc1ccccc1)=O 4 - High Confidence None 1.0 17.34 1.3016570284697508 0.95999999999999996 0.057000000000000002 2.0 0.16387961865883344

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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: 43.86 % / Mosaicity: 0.3 °
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: 1.62→21.67 Å / Num. obs: 40527 / % possible obs: 97.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.73 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.063 / Rrim(I) all: 0.148 / Net I/σ(I): 6.8 / Num. measured all: 220775 / Scaling rejects: 9
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
1.62-1.7250.6673195063750.6350.3240.7452.496.5
4.86-21.6760.0931001316780.9880.0420.10213.698.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1682refinement
Aimless0.3.6data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5AMF

5amf


Resolution: 1.62→21.67 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 2004 4.95 %
Rwork0.1968 38461 -
obs0.1987 40465 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.58 Å2 / Biso mean: 20.7485 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 1.62→21.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 47 269 2294
Biso mean--18.25 27.67 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072195
X-RAY DIFFRACTIONf_angle_d1.0642969
X-RAY DIFFRACTIONf_chiral_restr0.04321
X-RAY DIFFRACTIONf_plane_restr0.004397
X-RAY DIFFRACTIONf_dihedral_angle_d14.109916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.66050.30031450.29362583272893
1.6605-1.70540.31531780.28292691286998
1.7054-1.75550.30641560.26652733288999
1.7555-1.81220.30521480.24692747289599
1.8122-1.87690.29151530.22072748290199
1.8769-1.9520.23291460.22142756290299
1.952-2.04080.27781270.21352793292099
2.0408-2.14830.28911180.20592810292899
2.1483-2.28280.21391150.18682632274794
2.2828-2.45880.28021420.19652671281395
2.4588-2.70580.24561270.1972809293699
2.7058-3.09640.21431440.19452825296999
3.0964-3.89740.21511500.17212807295798
3.8974-21.67660.17681550.16152856301195

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