4PNJ | pdb_00004pnj

Recombinant Sperm Whale P6 Myoglobin Solved with Single Pulse Free Electron Laser Data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 
    0.188 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4PNJ

Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history

Literature

Goniometer-based femtosecond crystallography with X-ray free electron lasers.

Cohen, A.E.Soltis, S.M.Gonzalez, A.Aguila, L.Alonso-Mori, R.Barnes, C.O.Baxter, E.L.Brehmer, W.Brewster, A.S.Brunger, A.T.Calero, G.Chang, J.F.Chollet, M.Ehrensberger, P.Eriksson, T.L.Feng, Y.Hattne, J.Hedman, B.Hollenbeck, M.Holton, J.M.Keable, S.Kobilka, B.K.Kovaleva, E.G.Kruse, A.C.Lemke, H.T.Lin, G.Lyubimov, A.Y.Manglik, A.Mathews, I.I.McPhillips, S.E.Nelson, S.Peters, J.W.Sauter, N.K.Smith, C.A.Song, J.Stevenson, H.P.Tsai, Y.Uervirojnangkoorn, M.Vinetsky, V.Wakatsuki, S.Weis, W.I.Zadvornyy, O.A.Zeldin, O.B.Zhu, D.Hodgson, K.O.

(2014) Proc Natl Acad Sci U S A 111: 17122-17127

  • DOI: https://doi.org/10.1073/pnas.1418733111
  • Primary Citation Related Structures: 
    4PNJ

  • PubMed Abstract: 

    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.


  • Organizational Affiliation
    • Stanford Synchrotron Radiation Lightsource, HodgsonK@stanford.edu acohen@slac.stanford.edu.

Macromolecule Content 

  • Total Structure Weight: 18.75 kDa 
  • Atom Count: 1,790 
  • Modeled Residue Count: 154 
  • Deposited Residue Count: 154 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myoglobin154Physeter macrocephalusMutation(s): 0 
Gene Names: MB
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free:  0.188 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.309α = 90
b = 90.309β = 90
c = 45.204γ = 120
Software Package:
Software NamePurpose
cctbx.xfeldata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2014-12-17
    Changes: Database references
  • Version 1.3: 2015-04-01
    Changes: Other
  • Version 1.4: 2015-11-18
    Changes: Data collection
  • Version 1.5: 2017-11-15
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.6: 2018-11-28
    Changes: Data collection
  • Version 1.7: 2023-09-27
    Changes: Data collection, Database references, Refinement description