[English] 日本語
Yorodumi
- PDB-1ps5: STRUCTURE OF THE MONOCLINIC C2 FORM OF HEN EGG-WHITE LYSOZYME AT ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ps5
TitleSTRUCTURE OF THE MONOCLINIC C2 FORM OF HEN EGG-WHITE LYSOZYME AT 2.0 ANGSTROMS RESOLUTION
ComponentsLysozyme C
KeywordsHYDROLASE / GLYCOSIDASE
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMajeed, S. / Ofek, G. / Belachew, A. / Huang, C. / Zhou, T. / Kwong, P.D.
CitationJournal: Structure / Year: 2003
Title: Enhancing Protein Crystallization through Precipitant Synergy
Authors: Majeed, S. / Ofek, G. / Belachew, A. / Huang, C. / Zhou, T. / Kwong, P.D.
History
DepositionJun 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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
Remark 376 SPECIAL POSITION SULFATE 3001 IS ON A SPECIAL POSITION, WITH SULFUR 3001 ON THE B AXIS AND TWO OF ... SPECIAL POSITION SULFATE 3001 IS ON A SPECIAL POSITION, WITH SULFUR 3001 ON THE B AXIS AND TWO OF THE COORDINATING OXYGENS GENERATED BY ROTATION ABOUT THE TWO FOLD.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5233
Polymers14,3311
Non-polymers1922
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.944, 53.143, 50.211
Angle α, β, γ (deg.)90.00, 97.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3001-

SO4

-
Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: EGG / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 313 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M Lithium Sulfate, 8% MPD , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 313K
Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15-10 mg/mlprotein1drop
2350 mM1dropNaCl
32.5 mMTris1droppH7.1
40.02 %1dropNaN3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2001 / Details: OSMIC MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 7305 / Num. obs: 7305 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.072 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 7.4 / Num. unique all: 593 / Rsym value: 0.125 / % possible all: 79.7
Reflection
*PLUS

-
Processing

Software
NameVersionClassification
DENZO(DENZO)data reduction
SCALEPACK(DENZO)data scaling
CNS1.1refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IEE

1iee


Resolution: 2→18.74 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The special position sulfate was positioned by expanding the asymmetric unit to include the crystallographic 2-fold and refining in spacegroup C1. After the sulfate was positioned, ...Details: The special position sulfate was positioned by expanding the asymmetric unit to include the crystallographic 2-fold and refining in spacegroup C1. After the sulfate was positioned, refinement was completed in spacegroup C2 with the sulfate position fixed (and two of the four coordinating oxygens generated by 2-fold rotation about the crystallographic 2-fold).
RfactorNum. reflection% reflectionSelection details
Rfree0.25 397 5.4 %RANDOM
Rwork0.189 ---
all0.189 7305 --
obs0.189 7296 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9526 Å2 / ksol: 0.331572 e/Å3
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.45 Å20 Å2-0.68 Å2
2--11.86 Å20 Å2
3----6.4 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2→18.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 8 149 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.572.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 55 5.2 %
Rwork0.238 1007 -
obs-1072 83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 500 Å / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

+
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