9FCR | pdb_00009fcr

Crystal structure of RBBP9 with spacegroup p212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 
    0.234 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

A generic cross-seeding approach to protein crystallization.

Caspy, I.Tang, S.Bellini, D.Gorrec, F.

(2025) J Appl Crystallogr 58: 383-391

  • DOI: https://doi.org/10.1107/S1600576725000457
  • Primary Citation Related Structures: 
    9FCR

  • PubMed Abstract: 

    Obtaining diffraction-quality crystals is often the rate-limiting step during structure determination of biological macromolecules by X-ray crystallography. To address this problem, we investigated a cross-seeding approach with a mixture integrating a heterogeneous set of protein crystal fragments to be used as generic seeds. The fragments are nanometre-sized templates chosen to promote crystal nucleation of protein samples unrelated to the proteins forming the seeds. An atypical crystal form of the human serine hydrolase retinoblastoma binding protein 9 was obtained by adding the mixture to the protein sample before performing standard crystallization assays. The structure was solved by X-ray crystallography at 1.4 Å resolution. Follow-up experiments showed that crystal fragments of α-amylase were critical components in this particular result. The limitations and future applications of our experimental developments are discussed.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CambridgeCB2 0QH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 42.05 kDa 
  • Atom Count: 3,307 
  • Modeled Residue Count: 366 
  • Deposited Residue Count: 372 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine hydrolase RBBP9
A, B
186Homo sapiensMutation(s): 0 
Gene Names: RBBP9BOGRBBP10
EC: 3 (PDB Primary Data), 3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75884 (Homo sapiens)
Explore O75884 
Go to UniProtKB:  O75884
PHAROS:  O75884
GTEx:  ENSG00000089050 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75884
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free:  0.234 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.74α = 90
b = 82.55β = 90
c = 58.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references, Structure summary
  • Version 1.2: 2025-04-16
    Changes: Database references