5POR | pdb_00005por

PanDDA analysis group deposition -- Crystal Structure of BRD1 in complex with N10982a

• PDB DOI: https://doi.org/10.2210/pdb5POR/pdb
• Deposition Group: G_1002022 (changed state) | Explore  G_1002022  

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-07 Released: 2017-03-15 
• 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: 1.58 Å
• R-Value Free: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (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: 37 kDa 
• Atom Count: 2,344 
• Modeled Residue Count: 244 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 1	A, B	156	Homo sapiens	Mutation(s): 3  Gene Names: BRD1, BRL, BRPF2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens) Explore O95696  Go to UniProtKB:  O95696
PHAROS:  O95696 GTEx:  ENSG00000100425

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PW3	E [auth A], I [auth B]	4-acetyl-piperazin-2-one C6 H10 N2 O2 ISNPMTVERREURB-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.554	α = 90
b = 56.537	β = 90
c = 101.63	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-15 
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: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2017-10-04
  Changes: Structure summary
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2026-02-18
  Changes: Refinement description, Structure summary