Refinement of triclinic hen egg-white lysozyme at atomic resolution.

Walsh, M.A.; Schneider, T.R.; Sieker, L.C.; Dauter, Z.; Lamzin, V.S.; Wilson, K.S.

doi:10.2210/pdb3lzt/pdb

Macromolecule Content

Total Structure Weight: 14880.32
Atom Count: 1148
Residue Count: 129
Unique protein chains: 1

3LZT

REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION

DOI: 10.2210/pdb3LZT/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus

Deposited: 1997-03-23 Released: 1998-03-25
Deposition Author(s): Walsh, M.A., Schneider, T., Sieker, L.C., Dauter, Z., Lamzin, V., Wilson, K.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.925 Å
R-Value Free: 0.114

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Refinement of triclinic hen egg-white lysozyme at atomic resolution.

Walsh, M.A., Schneider, T.R., Sieker, L.C., Dauter, Z., Lamzin, V.S., Wilson, K.S.

(1998) Acta Crystallogr.,Sect.D 54: 522-546

PubMed: 9761848 Search on PubMed
Primary Citation of Related Structures:
4LZT
Also Cited By: 1HF4

PubMed Abstract:

X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F > 4sigma(F) for the low- and room-temperature structures, respectively. The estimated r.m.s. coordinate error is 0.032 A for protein atoms, 0.050 A for all atoms in the low-temperature study, and 0.038 A for protein atoms and 0.049 A for all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conformations. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.

Related Citations:

Refinement of Triclinic Lysozyme: II. The Method of Stereochemically Restrained Least Squares
Ramanadham, M.,Sieker, L.C.,Jensen, L.H.
(1990) Acta Crystallogr.,Sect.B 46: 63
Refinement of Triclinic Lysozyme: I. Fourier and Least-Squares Methods
Hodsdon, J.M.,Brown, G.M.,Sieker, L.C.,Jensen, L.H.
(1990) Acta Crystallogr.,Sect.B 46: 54

Organizational Affiliation:

European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany. walsh@anl.gov

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSOZYME	A	129	Gallus gallus	Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Go to Gene View: LYZ Go to UniProtKB: P00698
Protein Feature View Full Protein Feature View for P00698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
ACT Query on ACT Download SDF File Download CCD File	A	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
NO3 Query on NO3 Download SDF File Download CCD File	A	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Ligand Interaction