[English] 日本語
Yorodumi
- PDB-1lcn: Monoclinic hen egg white lysozyme, thiocyanate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lcn
TitleMonoclinic hen egg white lysozyme, thiocyanate complex
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / GLYCOSIDASE / LYSOZYME
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THIOCYANATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsHamiaux, C. / Prange, T. / Ducruix, A. / Vaney, M.C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structural effects of monovalent anions on polymorphic lysozyme crystals.
Authors: Vaney, M.C. / Broutin, I. / Retailleau, P. / Douangamath, A. / Lafont, S. / Hamiaux, C. / Prange, T. / Ducruix, A. / Ries-Kautt, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The Decameric Structure of Bovine Pancreatic Trypsin Inhibitor (BPTI) at 2.7 A Resolution.
Authors: Hamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A. / Lafont, S. / Astier, J.P. / Veesler, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structures of Monoclinic Lysozyme Iodide at 1.6 A and of Triclinic Lysozyme Nitrate at 1.1 A
Authors: Steinhauf, L.K.
#3: Journal: Biophys.Chem. / Year: 1998
Title: Characterization of the Interaction Between Bovine Pancreatic Trypsin Inhibitor and Thiocyanate by NMR
Authors: Jolivalt, C. / Bockmann, A. / Ries-Kautt, M. / Ducruix, A. / Guittet, E.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of Hexagonal Turkey Egg-White Lysozyme at 1.65 A Resolution
Authors: Howell, P.L.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of a Dimeric Form of Erabutoxin-B, Crystallized from a Thiocyanate Solution
Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A.
#6: Journal: J.Cryst.Growth / Year: 1991
Title: Crystallisation of Basic Proteins by Ion Pairing
Authors: Ries-Kautt, M. / Ducruix, A.
History
DepositionOct 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
B: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8375
Polymers28,6622
Non-polymers1743
Water2,450136
1
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4473
Polymers14,3311
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3892
Polymers14,3311
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.010, 63.180, 60.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97654, 0.1823, -0.11462), (-0.19144, 0.97868, -0.07443), (0.09861, 0.09463, 0.99062)
Vector: -16.78495, 2.84472, 26.00986)

-
Components

#1: Protein PROTEIN (LYSOZYME) / MURAMIDASE


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: SIGMA, USED AFTER ION-EXCHANGE PURIFICATION (DESALTING)
Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsLOOP 67-73 STANDS IN TWO DIFFERENT CONFORMATIONS IN MOLECULES A AND B, AND IS BETTER DEFINED IN ...LOOP 67-73 STANDS IN TWO DIFFERENT CONFORMATIONS IN MOLECULES A AND B, AND IS BETTER DEFINED IN MOLECULE A. ARG B 73 PLAYS AN IMPORTANT ROLE IN THE ALTERNATE CONFORMATION IN MOLECULE B: BEING INVOLVED IN A SALT BRIDGE WITH ASP B119 (OF A SYMMETRY RELATED MOLECULE), IT STANDS IN A DISALLOWED REGION OF THE RAMACHANDRAN PLOT. ALLOWS THE LOOP TO ADOPT ANOTHER CONFORMATION.
Nonpolymer details3 THIOCYANATE ANIONS ARE FOUND IN THE STRUCTURE. THEY ARE SPREAD OVER TWO SITES: SCN201 IS BOUND TO ...3 THIOCYANATE ANIONS ARE FOUND IN THE STRUCTURE. THEY ARE SPREAD OVER TWO SITES: SCN201 IS BOUND TO TYR B53, BUT NO DENSITY IS FOUND AT ITS EQUIVALENT POSITION IN MOLECULE A. SCN202 AND 203 ARE FOUND AT EQUIVALENT POSITION IN MOLECULE A AND B, BOUND TO LYS 116.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 33 %
Crystal growpH: 5 / Details: KSCN 190MM BUFFER CH3COOK 50MM, PH=5, pH 5.0
Crystal grow
*PLUS
Temperature: 291 K / pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.7 mg/mlprotein1drop
250 mMpotassium acetate1drop
3190 mM1dropKSCN

-
Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.963
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 1998 / Details: MIRROR
RadiationMonochromator: BENT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.963 Å / Relative weight: 1
ReflectionResolution: 1.63→15.83 Å / Num. obs: 25539 / % possible obs: 96.8 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.028 / Net I/σ(I): 15.2
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.121 / % possible all: 89.5
Reflection
*PLUS
Rmerge(I) obs: 0.028

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MONOMER A FROM 5LYM PDB ENTRY (MONOCLINIC LYSOZYME)

5lym


Resolution: 1.63→15.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2526 9.9 %RANDOM
Rwork0.198 ---
obs0.198 25515 96.9 %-
Displacement parametersBiso mean: 16.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.63→15.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 9 136 2147
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.07
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.581.5
X-RAY DIFFRACTIONx_mcangle_it2.512
X-RAY DIFFRACTIONx_scbond_it2.82
X-RAY DIFFRACTIONx_scangle_it4.252.5
LS refinement shellResolution: 1.63→1.69 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.304 233 9.9 %
Rwork0.284 2124 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SCNTOPH19.SCN
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.284

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more