2ANV

crystal structure of P22 lysozyme mutant L86M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Extension to 2268 atoms of direct methods in the ab initio determination of the unknown structure of bacteriophage P22 lysozyme.

Mooers, B.H.Matthews, B.W.

(2006) Acta Crystallogr.,Sect.D 62: 165-176

  • DOI: 10.1107/S0907444905037212
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray crystal structure of the previously unknown bacteriophage P22 lysozyme, the product of gene 19, has been determined ab initio by direct methods using the program SIR2002. The presence of several partially occupied iodine anions and samarium ...

    The X-ray crystal structure of the previously unknown bacteriophage P22 lysozyme, the product of gene 19, has been determined ab initio by direct methods using the program SIR2002. The presence of several partially occupied iodine anions and samarium cations augmented the ability of direct methods to locate all 2268 non-H protein atoms in the asymmetric unit, making this one of the largest structures to date to be determined ab initio. The iodides were introduced from a quick soak, which the crystal survived sufficiently well to diffract to 1.04 angstroms resolution. The complete heavy-atom substructure contributed 6.6% of the total scattering power. The initial determination of the structure assumed that there were two iodide ions in the asymmetric unit, although it was later determined that these sites correspond to partially occupied samarium ions. Tests suggested that it is better to overestimate rather than underestimate the heavy-atom content. While experimental phases from all of the successful tests were of high quality, the best results came from a SAD experiment using the programs SHELXD and SHELXE. Nonetheless, ab initio structure determination by direct methods was found to be a viable alternative to traditional protein crystallographic methods provided that the X-ray data extend to atomic resolution and heavy atoms with sufficient scattering power are present in the crystal.


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, OR 97403-1229, USA. blaine@uoxray.uoregon.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A, B
146Salmonella phage P22Mutation(s): 1 
Gene Names: 19
EC: 3.2.1.17
Find proteins for P09963 (Salmonella phage P22)
Go to UniProtKB:  P09963
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM
Query on SM

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A, B
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.122 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.013α = 90.00
b = 50.415β = 103.80
c = 46.587γ = 90.00
Software Package:
Software NamePurpose
SIR2002model building
MOSFLMdata reduction
SCALEPACKdata scaling
SCALAdata scaling
HKL-2000data reduction
SHELXL-97refinement
SIRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance