3LZT

REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION

DOI: 10.2210/pdb3LZT/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

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: 0.93 Å
R-Value Free: 0.114
R-Value Observed: 0.093

wwPDB Validation 3D 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 D Biol Crystallogr 54: 522-546

PubMed: 9761848 Search on PubMed
DOI: 10.1107/s0907444997013656
Primary Citation of Related Structures:
4LZT, 3LZT

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: I. Fourier and Least-Squares Methods
Hodsdon, J.M., Brown, G.M., Sieker, L.C., Jensen, L.H.
(1990) Acta Crystallogr B 46: 54

Refinement of Triclinic Lysozyme: II. The Method of Stereochemically Restrained Least Squares
Ramanadham, M., Sieker, L.C., Jensen, L.H.
(1990) Acta Crystallogr B 46: 63

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	129	Gallus gallus	Mutation(s): 0 Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A]	H [auth A], I [auth A], J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction