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- PDB-5ame: Crystal structure of the bromodomain of human surface epitope eng... -

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Basic information

Entry
Database: PDB / ID: 5ame
TitleCrystal structure of the bromodomain of human surface epitope engineered BRD1A in complex with 3D Consortium fragment 4-acetyl- piperazin-2-one (SGC - Diamond I04-1 fragment screening)
ComponentsBROMODOMAIN-CONTAINING PROTEIN 1
KeywordsTRANSCRIPTION / HISTONE-BINDING PROTEIN / BROMODOMAIN / EPIGENETIC / FRAGMENTSCREENING / STRUCTURAL GENOMICS CONSORTIUM / SGC / DIAMOND I04-1
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
4-acetyl-piperazin-2-one / Bromodomain-containing protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.578 Å
AuthorsPearce, N.M. / Fairhead, M. / Strain-Damerell, C. / Talon, R. / Wright, N. / Ng, J.T. / Bradley, A. / Cox, O. / Bowkett, D. / Collins, P. ...Pearce, N.M. / Fairhead, M. / Strain-Damerell, C. / Talon, R. / Wright, N. / Ng, J.T. / Bradley, A. / Cox, O. / Bowkett, D. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Krojer, T. / Burgess-Brown, N. / Brennan, P. / Arrowsmith, C.H. / Edwards, E. / Bountra, C. / von Delft, F.
CitationJournal: To be Published
Title: Crystal Structure of the Bromodomain of Human Surface Epitope Engineered Brd1A in Complex with 3D Consortium Fragment 4-Acetyl-Piperazin-2-One
Authors: Pearce, N.M. / Fairhead, M. / Strain-Damerell, C. / Talon, R. / Wright, N. / Ng, J.T. / Bradley, A. / Cox, O. / Bowkett, D. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Krojer, T. / ...Authors: Pearce, N.M. / Fairhead, M. / Strain-Damerell, C. / Talon, R. / Wright, N. / Ng, J.T. / Bradley, A. / Cox, O. / Bowkett, D. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Krojer, T. / Burgess-Brown, N. / Brennan, P. / Arrowsmith, C.H. / Edwards, E. / Bountra, C. / von Delft, F.
History
DepositionMar 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)31,6714
Polymers31,5062
Non-polymers1652
Water5,405300
1
A: BROMODOMAIN-CONTAINING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)15,7531
Polymers15,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BROMODOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9183
Polymers15,7531
Non-polymers1652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.554, 56.537, 101.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BROMODOMAIN-CONTAINING PROTEIN 1 / BRD1A / BR140-LIKE PROTEIN / BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 2


Mass: 15753.008 Da / Num. of mol.: 2 / Fragment: BROMODOMAIN AND PHD FINGER, RESIDUES 556-688 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SURFACE EPITOPE ENGINEERED P566E, V569R / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O95696
#2: Chemical ChemComp-PW3 / 4-acetyl-piperazin-2-one


Mass: 142.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O2
#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 / Water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details4-ACETYL-PIPERAZIN-2-ONE (PW3): 3D CONSORTIUM FRAGMENT, SGC NAMES N10982A FMO3D000294A
Sequence detailsEPITOPE ENGINEERED MUTATIONS P566E,V569R

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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: 2.57 Å3/Da / Density % sol: 52.17 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6.2
Details: 0.1M BIS-TRIS PH 6.2 , 31% PEG3350, 293 K, 12 HOURS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.58→29.06 Å / Num. obs: 44164 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 22.27 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.8
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE MODEL

Resolution: 1.578→29.059 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 21.24 / Stereochemistry target values: ML / Details: SGC - DIAMOND I04-1 FRAGMENT SCREENING
RfactorNum. reflection% reflection
Rfree0.2044 2146 4.9 %
Rwork0.1814 --
obs0.1826 44106 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.56 Å2
Refinement stepCycle: LAST / Resolution: 1.578→29.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 11 300 2284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132102
X-RAY DIFFRACTIONf_angle_d1.2962849
X-RAY DIFFRACTIONf_dihedral_angle_d13.888828
X-RAY DIFFRACTIONf_chiral_restr0.058314
X-RAY DIFFRACTIONf_plane_restr0.006382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5779-1.61460.30481240.28382732X-RAY DIFFRACTION97
1.6146-1.6550.28751220.25682690X-RAY DIFFRACTION96
1.655-1.69970.2271480.2472717X-RAY DIFFRACTION98
1.6997-1.74970.24661370.22852792X-RAY DIFFRACTION99
1.7497-1.80620.21251390.21652796X-RAY DIFFRACTION99
1.8062-1.87070.25281700.20172744X-RAY DIFFRACTION99
1.8707-1.94560.2661380.20722825X-RAY DIFFRACTION99
1.9456-2.03420.21521460.19642816X-RAY DIFFRACTION100
2.0342-2.14140.22011530.18422811X-RAY DIFFRACTION100
2.1414-2.27550.18521090.17042826X-RAY DIFFRACTION99
2.2755-2.45110.18061280.1762707X-RAY DIFFRACTION95
2.4511-2.69760.23011870.17722813X-RAY DIFFRACTION100
2.6976-3.08760.20331540.17622857X-RAY DIFFRACTION100
3.0876-3.88860.18931350.16332899X-RAY DIFFRACTION100
3.8886-29.06420.17631560.16832935X-RAY DIFFRACTION97
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)
11.1116-0.2909-0.14341.22150.51220.17050.24250.1873-0.0214-0.1122-0.2642-0.61320.01390.47620.16330.19010.0003-0.01160.36050.02740.37287.4218-2.6667.6656
21.4304-0.14460.10730.65480.12160.43680.1380.0063-0.0010.1135-0.0913-0.1401-0.16250.040200.225-0.02330.00080.19690.02270.1756-2.99044.65839.5137
30.3050.2428-0.1320.1525-0.21980.3570.02390.2496-0.15350.08860.10140.22040.03680.06520.01950.20620.01230.0090.2057-0.01790.1821-11.94762.387-2.0278
40.51610.3151-0.18340.1942-0.11190.1052-0.3424-0.0251-0.1497-0.0266-0.0106-1.19260.5598-0.0286-0.06860.40530.1228-0.14880.3131-0.00530.58642.6674-14.99427.9635
50.4712-0.1901-0.58270.31420.02620.81230.0289-0.1165-0.0410.08470.08440.0711-0.1113-0.19560.00020.1584-0.034-0.01060.1683-0.0010.1985-26.6268-4.410428.2775
60.13880.4538-0.33010.4958-0.27321.18660.03980.0532-0.0335-0.1298-0.0451-0.06140.25120.0959-00.18040.024-0.01010.15850.00530.1736-23.6325-4.521314.8466
70.20060.1747-0.09310.3831-0.27080.11260.06540.06680.0746-0.1087-0.0903-0.0211-0.0624-0.0414-0.00010.17270.0346-0.00410.16950.01450.1887-23.4379.875710.0288
80.1506-0.02370.14420.12670.0820.1758-0.10950.02150.16080.259-0.2257-0.4295-0.30040.5442-0.00060.2486-0.0443-0.04520.26780.02240.2473-16.45961.959332.367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 22:60)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 61:107)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 108:127)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 128:144)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 22:60)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 61:107)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 108:127)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 128:144)

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