Citations in PubMed

Primary Citation PubMed: 3586019 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 20

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Improved prediction of critical residues for protein function based on network and phylogenetic analyses.

(2005) BMC Bioinformatics 6

PubMed: 16124876 | PubMedCentral: PMC1208857 | DOI: 10.1186/1471-2105-6-213

The parameters used to run the Conseq server for 2LZM, 1BTL and 1HIV were: Maximum likelihood method used to calculate the conservation scores, PSI-BLAST E-value = 0.001, maximum number of homologous ... equences = 50 and the number of PSI-BLAST iterations = l (except for 2LZM, for which it was 3).

The Protein Data Bank (PDB) files used for each of these three proteins are respectively 1BTL, 1HIV and 2LZM [[ 13 , 14 ] and [ 15 ]].

Phylogenetic approaches Protein sequences from 2LZM, 1BTL, 1HIV, 1GVP, 1A2P and the set of 128 PDB proteins were aligned with their homologues using the Conseq server [ 18 ] or using the alignments provided for these three proteins in the Hssp database [ 22 , 23 ].

Publication Year: 2005


Efficient identification of critical residues based only on protein structure by network analysis.

(2007) PLoS One 2

PubMed: 17502913 | PubMedCentral: PMC1855080 | DOI: 10.1371/journal.pone.0000421

Briefly, the T4L-HIV-TEM1 set includes three enzymes that have been extensively characterized structurally and functionally (TEM1 beta-lactamase (PDB code 1BTL), HIV-1 protease (PDB code 1HIV) and T4 ... ysozyme (PDB code 2LZM)).

Publication Year: 2007


Stereochemical criteria for prediction of the effects of proline mutations on protein stability.

(2007) PLoS Comput Biol 3

PubMed: 18069886 | PubMedCentral: PMC2134964 | DOI: 10.1371/journal.pcbi.0030241

The WT protein structure (pdb id 2lzm) was used as the template in each case to generate the models.

Publication Year: 2007


Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.

(2008) BMC Bioinformatics 9

PubMed: 18366628 | PubMedCentral: PMC2292695 | DOI: 10.1186/1471-2105-9-148

The native structures for the folded state were taken from the Protein Data Bank (PDB) [ 54 ] with the structure codes 2LZM, 2RN2 and 1STN, respectively.

These structures were extracted from various positions in the X-ray structures of 6 different proteins taken from the PDB [ 54 ]: lysozyme (2LZM), bovine pancreatic trypsin inhibitor (4PTI), staphylococcal nuclease (1STN), α -toxin (1PTX), ribonuclease A (2RN2) and cyclophilin (2CPL).

Publication Year: 2008


Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs.

(2010) PLoS One 5

PubMed: 21085702 | PubMedCentral: PMC2976769 | DOI: 10.1371/journal.pone.0015388

The protein colour scheme is grey for GH19 structure (protein code: 3cql), purple for GH22c (1iee), green for GH22i (2dqa), brown for GH23 (153l), yellow for GH24v (2lzm), blue for GH24l (1am7) and aq... amarine for GH46 (1qgi).

Publication Year: 2010


Discovering conformational sub-states relevant to protein function.

(2011) PLoS One 6

PubMed: 21297978 | PubMedCentral: PMC3030567 | DOI: 10.1371/journal.pone.0015827

Lysozyme Simulations MD simulation for T4 lysozyme were initiated from the crystal structure 2LZM [46] .

Publication Year: 2011


Toward the estimation of the absolute quality of individual protein structure models.

(2011) Bioinformatics 27

PubMed: 21134891 | PubMedCentral: PMC3031035 | DOI: 10.1093/bioinformatics/btq662

Z -score analysis of the T4 bacteriophage lysozyme (2lzm, chain A) and the Dengue virus NS3 serine protease (1bef, chain A) PDB QMEAN C-β All-atom Solvation Torsion T4 lysozyme, 2lzm 0.5 0.6 1... 1 0.7 −0.3 Serine protease, 1bef −5.5 −3.4 −3.6 −2.7 −4.1 Both the QMEAN Z -score as well as the Z -scores of individual statistical potential terms are reported.

Table 1 and Supplementary Figure S5 show the Z -scores analysis of two experimental structures solved by X-ray diffraction: bacteriophage T4 lysozyme [PDB:2lzm, ( Weaver and Matthews, 1987 )] and Dengue virus NS3 serine protease [PDB:1bef, (2009; Murthy et al. , 1999 )].

Publication Year: 2011


KINARI-Web: a server for protein rigidity analysis.

(2011) Nucleic Acids Res 39

PubMed: 21693559 | PubMedCentral: PMC3125808 | DOI: 10.1093/nar/gkr482

We illustrate the curation feature on PDB file 2LZM, Bacteriophage T4 Lysozyme.

Publication Year: 2011


MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL.

(2012) Appl Magn Reson 42

PubMed: 22448103 | PubMedCentral: PMC3296949 | DOI: 10.1007/s00723-012-0314-0

Table 1 EPR-derived distances of spin-labeled T4L (PDB entry 2LZM, [ 33 ]) compared to predictions from mtsslWizard and MMM in 298K and 175K mode AA EPR < r >/ r pk Cβ&... x02013;Cβ MtsslWizard < r >/ r pk MMM 298 K < r >/ r pk MMM 175 K < r >/ r pk 061–135 d 47.2/– 40 49/50 47/47 46/46 065–135 d 46.3/– 37 47/47 44/44 42/41 061–086 d 37.5/– 37 45/46 42/43 41/42 065–086 d 37.4/– 31 37/38 36/36 33/30 080–135 d 36.8/– 27 36/38 33/36 32/35 061–080 d 34/– 29 34/33 31/31 31/31 065–080 d 26.5/– 22 25/24 24/24 23/23 119–131 b 25/– 13 24/25 19/23 18/17 123–131 b 23/– 14 24/25 20/22 19/19 065–076 d 21.4/– 17 18/19 19/20 18/16 116–131 b 19/– 11 18/19 17/20 17/20 119–128 b 19/– 9.7 18/19 16/19 15/12 140–151 b 18/– 17 21/21 21/20 19/20 089–093 b 16/– 12 17/17 18/16 18/18 086–119 b 15/– 10 13/12 16/14 16/17 120–131 b 14/– 9 12/12 (120: vdW 3.2, t) a 14/13 14/14 127–151 b 14/– 12 14/14 16/17 16/18 59/159 c 41.9/42 34 43/43 40/40 38/40 60/90 c 37.8/38 37 45/46 44/45 43/42 60/94 c 25.5/26 28 31/32 33/33 33/36 60/109 c 35.2/34 31 39/40 35/36 34/33 60/154 c 34.1/34 34 38/39 (154: t) 38/40 40/42 62/134 c 41.1/41 36 48/48 (both: t) 44/47 46/47 64/122 c 34.1/33 33 38/38 38/38 38/39 82/94 c 30.7/32 24 32/33 31/31 29/31 82/132 c 26.3/29 21 28/27 26/27 25/25 82/155 c 35.8/38 28 38/39 35/37 33/31 83/123 c 20.5/21 15 17/17 19/21 18/15 93/112 c 26.1/26 21 32/33 (112:vdW3.2, t) 30/32 29/31 93/123 c 24.8/25 19 26/27 25/26 24/24 93/154 c 25.1/25 16 26/27 (154:t) 23/25 21/23 94/132 c 31.7/32 19 32/33 (both: t) 29/31 27/29 108/155 c 35.2/36 25 37/37 34/36 32/32 109/134 c 30.6/31 21 31/33 28/31 27/25 115/155 c 28.2/27 23 33/33 29/30 26/27 116/134 c 20.2/20 12 17/17 18/20 17/17 Distances are given in angström. MtsslWizard was run with default parameters (“normal search”, “vdW cutoff: 3.4”, “allowed clashes: 0”) if not stated otherwise.

Publication Year: 2012


Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noise.

(2012) Acta Crystallogr A 68

PubMed: 22514069 | PubMedCentral: PMC3329770 | DOI: 10.1107/S010876731200493X

The former (Weaver & Matthews, 1987 ▶ ) (PDB code 2lzm , number of residues 164, molecular length 60 Å) is chosen as a typical small globular protein.

Publication Year: 2012


RosettaEPR: rotamer library for spin label structure and dynamics.

(2013) PLoS One 8

PubMed: 24039810 | PubMedCentral: PMC3764097 | DOI: 10.1371/journal.pone.0072851

Double Mutant MTSSL Conformational Sampling A pseudo wild type starting structure was created as described above whereby cysteine residues 54 and 97 of PDB ID 2LZM were computationally mutated to thre... nine and alanine, respectively.

Residues at 162 exposed sites on the primarily α-helical T4 lysozyme (PDBid 2LZM) and β-strand chitinase (PDBid 2CWR) [37] proteins were computationally mutated to create 162 single spin labeled mutants.

Therefore, the single mutants for these were computationally created from the T4 lysozyme crystal structure with PDB ID 2LZM [45] .

The pseudo-wildtype structure described in “ Experimental Procedures ” based on the crystal structure with PDB ID 2LZM was computationally mutated to contain a spin label at site 118 and relaxed ten times.

Publication Year: 2013


Rigidity analysis of protein biological assemblies and periodic crystal structures.

(2013) BMC Bioinformatics 14 Suppl 18

PubMed: 24564201 | PubMedCentral: PMC3817814 | DOI: 10.1186/1471-2105-14-S18-S2

The number of significant rigid clusters increase in crystal lattice - PDB File 1UCS In the previous case study we obtained a very rigid crystal of PDB file 2LZM, with a very large dominant cluster.

Publication Year: 2013


Three-dimensional electron crystallography of protein microcrystals.

(2013) Elife 2

PubMed: 24252878 | PubMedCentral: PMC3831942 | DOI: 10.7554/eLife.01345

Models for molecular replacement validation DOI: http://dx.doi.org/10.7554/eLife.01345.016 Protein PDB ID Molecular weight (kDa) Symmetry Unit cell dimensions MR solution Hen Egg White Lysozyme * 4AXT... 14.3 P4 3 2 1 2 a = b = 78.24 Å Yes c = 37.47 Å α = β = γ = 90° T4 Lysozyme † 2LZM 18.7 P3 2 12 a = b = 61.20 Å No c = 96.80 Å α = β = 90° γ = 120° Calmodulin ‡ 3CLN 16.7 P1 a = 29.71 Å, No b = 53.79 Å, c = 24.99 Å α = 94.13°, β = 97.57°, γ = 89.46° Dodecin § 4B2J 8.5 F4 1 32 a = b = c = 142.90 Å No α = β = γ = 90° αA Crystallin # 3L1E 11.9 P4 1 2 1 2 a = b = 56.22 Å, No c = 68.66 Å α = β = γ = 90° * Cipriani et al. (2012) .

Publication Year: 2013


A conservation and rigidity based method for detecting critical protein residues.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24565061 | PubMedCentral: PMC3952096 | DOI: 10.1186/1472-6807-13-S1-S6

The other protein that we examined is Lysozyme from bacteriophage T4 (PDB ID 2lzm ).

Publication Year: 2013


CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations.

(2014) J Chem Inf Model 54

PubMed: 24624945 | PubMedCentral: PMC3985889 | DOI: 10.1021/ci500007n

Test Systems The PDB IDs of all the proteins used in this work are 2A3D (α3D: a de novo designed single-chain three-helix bundle); 29 2KBG (Fibronectin: the second Fibronectin type-III module ... f NCAM2); 2LZM (bacteriophage T4 lysozyme); 30 2KSJ (Pf1 coat protein: the major coat protein of Pf1 bacteriophage); 31 2L35 (the DAP12-NKG2C transmembrane heterotrimer); 32 1G90 (OmpA: outer membrane protein A); 33 1AFO (GpA: dimeric transmembrane domain of human glycophorin A); 34 2K4T (VDAC: the voltage-dependent anion channel); 35 2OAR (MscL: mechanosensitive channel of large conductance); 36 and 2OMF (OmpF: outer membrane protein F).

Publication Year: 2014


Distance measurement between two flexible sites in proteins in high viscosity medium at physiological temperature using continuous wave EPR.

(2014) Protein Cell 5

PubMed: 24643643 | PubMedCentral: PMC3996158 | DOI: 10.1007/s13238-014-0040-5

From the crystal structure of T4L (PDB code 2LZM), residue 90 is in a loop region exposed to solvent, while residue 117 is found in a helix boundary facing the interior of the protein (Fig.

Publication Year: 2014


TSpred: a web server for the rational design of temperature-sensitive mutants.

(2014) Nucleic Acids Res 42

PubMed: 24782523 | PubMedCentral: PMC4086094 | DOI: 10.1093/nar/gku319

Ts mutant position as predicted by sequence-based, structured-based or both methods Protein PDB ID Chain length Residue position Residue type Prediction method gene V 1YHA 87 35 VAL Both 45 VAL Both 4... ILE Structure 63 VAL Structure 81 LEU Structure 78 ILE Sequence lambda repressor 1LMB 92 51 PHE Both 65 LEU Both 76 PHE Both 84 ILE Both 18 LEU Structure 36 VAL Structure 47 VAL Structure T4 lysozyme 2LZM 164 6 MET Both 102 MET Both 149 VAL Structure 153 PHE Structure 103 VAL Sequence CcdB 3VUB 101 17 PHE Both 18 VAL Both 33 VAL Both 34 ILE Both 54 VAL Both 5 VAL Structure 36 LEU Structure 63 MET Structure 50 LEU Sequence 53* VAL Sequence 96 LEU Sequence 97 MET Sequence 98 PHE Sequence Gal4 3COQ 88 68 PHE Both 69 LEU Sequence 70 LEU Sequence Ura3 1DQW 267 25 MET Structure 32 LEU Structure 118 ILE Structure The wild-type residue (three-letter amino acid code) at the position is listed under residue type.

The proteins were gene V (PDB: 1YHA), lambda repressor (PDB: 1LMB), T4 Lysozyme (PDB: 2LZM), CcdB (PDB: 3VUB), Gal4 (PDB: 3CQQ) and Ura3 (PDB: 1DQW)) ( 13 , 23 , 44–49 ).

The templates were identified by searching DBAli ( http://www.salilab.org/DBAli/ ) ( 50 ) for structures similar to T4 lysozyme (PDB 2LZM).

Publication Year: 2014


Stability curve prediction of homologous proteins using temperature-dependent statistical potentials.

(2014) PLoS Comput Biol 10

PubMed: 25032839 | PubMedCentral: PMC4102405 | DOI: 10.1371/journal.pcbi.1003689

( b ) 1am7 ( Bacteriophage lambda , 37 ), 2lzm ( Escherichia coli , 37 ), 1lz1 ( Homo sapiens , 37 ), 1am7 ( Gallus gallus , 41 ).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4196733

(A) Models of T4L both with (left) and without (right) peptidoglycan bound to the active site (PDB entries 150L and 2LZM, respectively).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4443714

The SPOA1,2–APAR::lysozyme structures were solved by molecular replacement in Phaser-MR using the experimentally phased cognate SPOA1,2 structure and T4 lysozyme (PDB 2LZM).

Publication Year: 2015