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- PDB-5pyg: PanDDA analysis group deposition -- Crystal Structure of SP100 af... -

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Basic information

Entry
Database: PDB / ID: 5pyg
TitlePanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 76)
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 / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein export from nucleus / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / negative regulation of DNA binding ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein export from nucleus / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / negative regulation of DNA binding / response to type II interferon / DNA damage response, signal transduction by p53 class mediator / regulation of angiogenesis / type II interferon-mediated signaling pathway / retinoic acid receptor signaling pathway / SUMOylation of DNA damage response and repair proteins / response to retinoic acid / telomere maintenance / nuclear periphery / response to cytokine / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / Interferon gamma signaling / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / protein domain specific binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / 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 / nucleus / cytoplasm
Similarity search - Function
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 ...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 / Bromodomain-like / Histone Acetyltransferase; Chain A / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nuclear autoantigen Sp-100
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.95 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 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 1.2Mar 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

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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)43,64410
Polymers42,9972
Non-polymers6468
Water10,431579
1
A: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9526
Polymers21,4991
Non-polymers4545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6914
Polymers21,4991
Non-polymers1933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.720, 45.410, 83.600
Angle α, β, γ (deg.)90.000, 102.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1063-

HOH

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Components

#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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.75 Å3/Da / Density % sol: 55.35 % / Mosaicity: 0 °
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: 1.95→42.67 Å / Num. obs: 33337 / % possible obs: 96.9 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.058 / Rrim(I) all: 0.108 / Net I/σ(I): 11.3 / Num. measured all: 111962 / Scaling rejects: 0
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
1.95-23.30.652811524490.6870.4270.784297.2
8.72-42.673.40.03614184160.9970.0230.04336.998.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0135refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4PTB

4ptb


Resolution: 1.95→42.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.478 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1639 4.9 %RANDOM
Rwork0.1765 ---
obs0.1791 31697 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.91 Å2 / Biso mean: 37.854 Å2 / Biso min: 15.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0 Å20.3 Å2
2---0.16 Å2-0 Å2
3---1.1 Å2
Refinement stepCycle: final / Resolution: 1.95→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 25 579 3529
Biso mean--55.17 52.45 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193125
X-RAY DIFFRACTIONr_bond_other_d0.0020.022888
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9364223
X-RAY DIFFRACTIONr_angle_other_deg1.0636681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72815574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3071524
X-RAY DIFFRACTIONr_chiral_restr0.1230.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023560
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02792
X-RAY DIFFRACTIONr_mcbond_it4.0413.5651452
X-RAY DIFFRACTIONr_mcbond_other4.0363.561451
X-RAY DIFFRACTIONr_mcangle_it6.265.3151820
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 131 -
Rwork0.274 2315 -
all-2446 -
obs--96.41 %

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