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- PDB-5myg: Crystal structure of the bromodomain of human BRPF1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5myg
TitleCrystal structure of the bromodomain of human BRPF1 in complex with NI-57 chemical probe
ComponentsPeregrin
KeywordsTRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD 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. ...BRPF1, PHD domain / Peregrin, ePHD 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 C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTallant, C. / Igoe, N. / Bayle, E.D. / Krojer, T. / Nunez-Alonso, G. / Kopec, J. / Fitzpatrick, F. / Savitsky, P. / Fedorov, O. / Brennan, P.E. ...Tallant, C. / Igoe, N. / Bayle, E.D. / Krojer, T. / Nunez-Alonso, G. / Kopec, J. / Fitzpatrick, F. / Savitsky, P. / Fedorov, O. / Brennan, P.E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Fish, P. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2017
Title: Design of a Chemical Probe for the Bromodomain and Plant Homeodomain Finger-Containing (BRPF) Family of Proteins.
Authors: Igoe, N. / Bayle, E.D. / Tallant, C. / Fedorov, O. / Meier, J.C. / Savitsky, P. / Rogers, C. / Morias, Y. / Scholze, S. / Boyd, H. / Cunoosamy, D. / Andrews, D.M. / Cheasty, A. / Brennan, P. ...Authors: Igoe, N. / Bayle, E.D. / Tallant, C. / Fedorov, O. / Meier, J.C. / Savitsky, P. / Rogers, C. / Morias, Y. / Scholze, S. / Boyd, H. / Cunoosamy, D. / Andrews, D.M. / Cheasty, A. / Brennan, P.E. / Muller, S. / Knapp, S. / Fish, P.V.
History
DepositionJan 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peregrin
B: Peregrin
C: Peregrin
D: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3488
Polymers54,8154
Non-polymers1,5344
Water1,36976
1
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0872
Polymers13,7041
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0872
Polymers13,7041
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0872
Polymers13,7041
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0872
Polymers13,7041
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.140, 123.716, 137.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 13703.698 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Chemical
ChemComp-LS8 / 4-cyano-~{N}-(1,3-dimethyl-2-oxidanylidene-quinolin-6-yl)-2-methoxy-benzenesulfonamide


Mass: 383.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H17N3O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M ammonium acetate, 17% PEG 10K, 0.1 M bis-tris pH 5.5
PH range: 5.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→28.88 Å / Num. obs: 28990 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 31.549 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.051 / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4116 / Rpim(I) all: 0.292 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1682refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 2.3→28.877 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.42
RfactorNum. reflection% reflection
Rfree0.3071 1445 5.04 %
Rwork0.2469 --
obs0.2498 28659 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 108 76 3929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013937
X-RAY DIFFRACTIONf_angle_d1.3445322
X-RAY DIFFRACTIONf_dihedral_angle_d14.2771572
X-RAY DIFFRACTIONf_chiral_restr0.06558
X-RAY DIFFRACTIONf_plane_restr0.007798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.299-2.38110.34211510.30092640X-RAY DIFFRACTION99
2.3811-2.47640.3641440.27862755X-RAY DIFFRACTION100
2.4764-2.58910.32691520.26452652X-RAY DIFFRACTION100
2.5891-2.72550.33941570.26722711X-RAY DIFFRACTION100
2.7255-2.89610.33231380.26772749X-RAY DIFFRACTION100
2.8961-3.11940.31641430.27532739X-RAY DIFFRACTION100
3.1194-3.43290.3211490.25962747X-RAY DIFFRACTION100
3.4329-3.92860.40211290.30492490X-RAY DIFFRACTION90
3.9286-4.94560.25431370.1962765X-RAY DIFFRACTION98
4.9456-28.87950.19971450.17432966X-RAY DIFFRACTION100
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)
11.96731.3596-0.64662.058-1.39742.2420.1365-0.1829-0.1153-0.0244-0.30220.0911-0.15250.29420.14710.2990.0766-0.06570.2045-0.05880.2778-1.823212.782-22.4843
22.25440.69180.38250.92540.41523.80160.03110.27880.2491-0.1766-0.08210.1934-0.09840.00430.02140.31880.1010.0290.2565-0.08770.2916-16.3159-13.2409-41.4512
32.18621.3142-1.10452.2357-1.08743.57350.0965-0.10940.10480.0174-0.15220.1232-0.09750.12260.05830.2761-0.05270.02130.4049-0.00880.26116.229624.6558-3.4146
42.31671.53440.92212.2813-0.05932.36910.1434-0.21020.13390.0416-0.01090.08070.29260.0715-0.09730.27720.0178-0.01980.3138-0.12080.259612.6211-24.6615-22.445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 626:740)
2X-RAY DIFFRACTION2(chain B and resid 626:740)
3X-RAY DIFFRACTION3(chain C and resid 629:740)
4X-RAY DIFFRACTION4(chain D and resid 630:740)

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