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- PDB-5enc: Crystal structure of the second bromodomain of Pleckstrin homolog... -

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Basic information

Entry
Database: PDB / ID: 5enc
TitleCrystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with N-(2,6-Dichlorobenzyl)acetamide (SGC - Diamond I04-1 fragment screening)
ComponentsPH-interacting protein
KeywordsSIGNALING PROTEIN / bromodomain / PHIP / crystallographic fragment screen / Structural Genomics / Structural Genomics Consortium / SGC / transcription
Function / homology
Function and homology information


regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / regulation of protein phosphorylation / RHOBTB2 GTPase cycle / : / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / insulin receptor binding / insulin receptor signaling pathway ...regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / regulation of protein phosphorylation / RHOBTB2 GTPase cycle / : / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / insulin receptor binding / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / BRWD/PHIP ancillary domain-like domain / BRWD1-like, N-terminal domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain ...: / BRWD/PHIP ancillary domain-like domain / BRWD1-like, N-terminal domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
~{N}-[[2,6-bis(chloranyl)phenyl]methyl]ethanamide / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsKrojer, T. / Talon, R. / Collins, P. / Bradley, A. / Cox, O. / Szykowska, A. / Burgess-Brown, N. / Brennan, P. / Bountra, C. / Arrowsmith, C.H. ...Krojer, T. / Talon, R. / Collins, P. / Bradley, A. / Cox, O. / Szykowska, A. / Burgess-Brown, N. / Brennan, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: Chem Sci / Year: 2016
Title: A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain.
Authors: Cox, O.B. / Krojer, T. / Collins, P. / Monteiro, O. / Talon, R. / Bradley, A. / Fedorov, O. / Amin, J. / Marsden, B.D. / Spencer, J. / von Delft, F. / Brennan, P.E.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9374
Polymers15,5951
Non-polymers3423
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint5 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.687, 91.582, 24.033
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PH-interacting protein / PHIP / IRS-1 PH domain-binding protein / WD repeat-containing protein 11


Mass: 15594.661 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1315-1440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHIP, WDR11 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-5QD / ~{N}-[[2,6-bis(chloranyl)phenyl]methyl]ethanamide


Mass: 218.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9Cl2NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5 , 0.15M magnesium chloride , 32% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92001 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 1.59→28.8 Å / Num. obs: 18820 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Net I/σ(I): 21.8 / Num. measured all: 120066
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.59-1.636.20.7262.4833913430.7910.31498.7
7.11-28.85.50.03653.114412640.9990.01798.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MB3

3mb3


Resolution: 1.59→28.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.491 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 933 5 %RANDOM
Rwork0.2035 ---
obs0.2057 17845 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.92 Å2 / Biso mean: 31.014 Å2 / Biso min: 19.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0 Å20 Å2
2--1.65 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.59→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 21 180 1219
Biso mean--44.18 40.34 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191070
X-RAY DIFFRACTIONr_bond_other_d0.0020.02978
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9591440
X-RAY DIFFRACTIONr_angle_other_deg1.02432258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79623.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98215188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.797159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
X-RAY DIFFRACTIONr_mcbond_it1.342.074500
X-RAY DIFFRACTIONr_mcbond_other1.3392.076501
X-RAY DIFFRACTIONr_mcangle_it2.0863.109628
LS refinement shellResolution: 1.589→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 52 -
Rwork0.269 1290 -
all-1342 -
obs--98.82 %
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)
11.88893.5208-1.64797.4994-3.6461.790.0253-0.1026-0.13620.1162-0.1726-0.3039-0.06180.07550.14730.052-0.03580.01140.0438-0.0260.12028.618620.4281-11.3141
23.16720.6544-0.30380.16790.10011.01660.0802-0.14420.23370.005-0.02420.023-0.02930.0107-0.0560.0881-0.0214-0.01320.0147-0.02620.1151-6.529716.982-5.3996
31.52780.5782-0.0793.34541.22090.5045-0.1574-0.17480.02980.25310.06880.24110.13490.06140.08870.1124-0.03820.01070.10130.01750.02-22.26762.0986-5.5145
41.93121.00920.55070.54330.40051.321-0.05090.1058-0.11230.00790.0403-0.0740.1886-0.1840.01070.1213-0.0256-0.04080.0489-0.02990.0854-10.35095.6451-10.5925
53.52191.4299-0.41360.70220.10990.7109-0.04370.23530.1641-0.03080.06390.0425-0.0089-0.1057-0.02010.057-0.0248-0.00080.03730.02820.1275-10.438715.0864-16.7983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1313 - 1319
2X-RAY DIFFRACTION2A1320 - 1334
3X-RAY DIFFRACTION3A1335 - 1356
4X-RAY DIFFRACTION4A1357 - 1395
5X-RAY DIFFRACTION5A1396 - 1436

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