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- PDB-5pwc: PanDDA analysis group deposition -- Crystal Structure of SP100 in... -

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Basic information

Entry
Database: PDB / ID: 5pwc
TitlePanDDA analysis group deposition -- Crystal Structure of SP100 in complex with E48115b
ComponentsNuclear autoantigen Sp-100
KeywordsTRANSCRIPTION / PanDDA / SGC - Diamond I04-1 fragment screening / bromodomain / epigenetics / XChemExplorer
Function / homology
Function and homology information


regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / negative regulation of endothelial cell migration / regulation of extrinsic apoptotic signaling pathway via death domain receptors / type I interferon-mediated signaling pathway / response to type II interferon ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / negative regulation of endothelial cell migration / regulation of extrinsic apoptotic signaling pathway via death domain receptors / type I interferon-mediated signaling pathway / response to type II interferon / negative regulation of DNA binding / DNA damage response, signal transduction by p53 class mediator / retinoic acid receptor signaling pathway / regulation of angiogenesis / SUMOylation of DNA damage response and repair proteins / type II interferon-mediated signaling pathway / response to retinoic acid / telomere maintenance / nuclear periphery / response to cytokine / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / protein dimerization activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / negative regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily ...Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,4-dichloro-N-(pyridin-3-yl)benzamide / SP100 nuclear antigen / Nuclear autoantigen Sp-100
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.549 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 / Category: chem_comp_atom / chem_comp_bond / database_2
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: Nuclear autoantigen Sp-100
B: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,21013
Polymers42,9972
Non-polymers1,21311
Water9,170509
1
A: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2167
Polymers21,4991
Non-polymers7176
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9946
Polymers21,4991
Non-polymers4955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.740, 45.415, 83.292
Angle α, β, γ (deg.)90.000, 102.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nuclear autoantigen Sp-100 / Nuclear dot-associated Sp100 protein / Speckled 100 kDa


Mass: 21498.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SP100 / Production host: Escherichia coli (E. coli) / References: UniProt: P23497, UniProt: H0Y4R8*PLUS

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Non-polymers , 6 types, 520 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-W77 / 2,4-dichloro-N-(pyridin-3-yl)benzamide


Mass: 267.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H8Cl2N2O
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details yes c1cc(cnc1)NC(c1ccc(cc1[Cl])[Cl])=O None 33.0491790152 9.84925881428 9.84925881428 c1cc(cnc1) ... yes c1cc(cnc1)NC(c1ccc(cc1[Cl])[Cl])=O 33.0491790152 9.84925881428 9.84925881428 c1cc(cnc1)NC(c1ccc(cc1[Cl])[Cl])=O 4 - High Confidence None 0.49 39.14411764705882 1.4171312559839073 0.873 0.17899999999999999 0.80000000000000004 0.33551102375156583 -0.955174674552 14.8757830823 14.8757830823 c1cc(cnc1)NC(c1ccc(cc1[Cl])[Cl])=O 4 - High Confidence None 0.4 38.30823529411765 1.657973671054824 0.85799999999999998 0.21299999999999999 1.3999999999999999 0.4299778380061823

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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: 2.75 Å3/Da / Density % sol: 55.2 % / Mosaicity: 0.04 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MES pH 6.1 -- 20% PEG20K

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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: Apr 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.55→28.44 Å / Num. obs: 66721 / % possible obs: 98 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Net I/σ(I): 12 / Num. measured all: 231376 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.590.7261605447600.630.460.8631.795.5
6.93-28.440.03627368000.9970.0230.04337.197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1682refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4PTB

4ptb


Resolution: 1.549→28.44 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 3333 5 %
Rwork0.1796 63384 -
obs0.1811 66717 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.32 Å2 / Biso mean: 28.2007 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 1.549→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 79 512 3433
Biso mean--37.19 39.26 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123082
X-RAY DIFFRACTIONf_angle_d1.2134160
X-RAY DIFFRACTIONf_chiral_restr0.057419
X-RAY DIFFRACTIONf_plane_restr0.006541
X-RAY DIFFRACTIONf_dihedral_angle_d14.4221260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5486-1.57070.33141300.28082524265493
1.5707-1.59410.27081390.26132581272098
1.5941-1.6190.24281470.24682649279698
1.619-1.64560.25561240.23072642276699
1.6456-1.6740.25661580.23012645280398
1.674-1.70440.26141400.23132614275498
1.7044-1.73720.25941320.22392695282798
1.7372-1.77260.27131640.22632582274698
1.7726-1.81120.25771450.21612680282599
1.8112-1.85330.27381310.21212635276699
1.8533-1.89960.26251280.19662688281699
1.8996-1.9510.22691260.19592641276799
1.951-2.00840.2121630.19442624278798
2.0084-2.07320.22481500.1962630278098
2.0732-2.14720.22991170.18992479259692
2.1472-2.23320.22321350.18062599273496
2.2332-2.33480.20291300.17282693282399
2.3348-2.45780.21741600.18092673283399
2.4578-2.61170.22641380.17332706284499
2.6117-2.81320.19941310.17342689282099
2.8132-3.0960.21651400.1752688282899
3.096-3.54320.18171350.16282680281598
3.5432-4.46130.17561170.14232571268893
4.4613-28.44780.17391530.16782776292998

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