5PYL | pdb_00005pyl

PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 81)

• PDB DOI: https://doi.org/10.2210/pdb5PYL/pdb
• Deposition Group: G_1002025 (ground state) | Explore  G_1002025  

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-08 Released: 2017-03-22 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.209 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

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.

(2017) Nat Commun 8: 15123-15123

• PubMed: 28436492 
• DOI: https://doi.org/10.1038/ncomms15123
• Primary Citation Related Structures: 
  5PB7, 5PB8, 5PB9, 5PBA, 5PBB, 5PBC, 5PBD, 5PBE, 5PBF, 5PBG, 5PBH, 5PBI, 5PBJ, 5PBK, 5PBL, 5PBM, 5PBN, 5PBO, 5PBP, 5PBQ, 5PBR, 5PBS, 5PBT, 5PBU, 5PBV, 5PBW, 5PBX, 5PBY, 5PBZ, 5PC0, 5PC1, 5PC2, 5PC3, 5PC4, 5PC5, 5PC6, 5PC7, 5PC8, 5PC9, 5PCA, 5PCB, 5PCC, 5PCD, 5PCE, 5PCF, 5PCG, 5PCH, 5PCI, 5PCJ, 5PCK, ... Search all related entries


• PubMed Abstract: 
  

  In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.

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Organizational Affiliation: 
• Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK.
Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK.
Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK.
UCB Pharma, 208 Bath Road, Slough SL1 3WE, UK.
Department of Statistics, University of Oxford, 24-29 St Giles, Oxford OX1 3LB, UK.
Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.64 kDa 
• Atom Count: 3,620 
• Modeled Residue Count: 355 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear autoantigen Sp-100	A, B	180	Homo sapiens	Mutation(s): 0  Gene Names: SP100
UniProt & NIH Common Fund Data Resources
Find proteins for P23497 (Homo sapiens) Explore P23497  Go to UniProtKB:  P23497
PHAROS:  P23497 GTEx:  ENSG00000067066

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.209 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.56	α = 90
b = 45.46	β = 101.85
c = 83.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references
• Version 1.3: 2026-02-18
  Changes: Refinement description, Structure summary