[English] 日本語
Yorodumi
- PDB-4baf: Hen egg-white lysozyme structure in complex with the europium tri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4baf
TitleHen egg-white lysozyme structure in complex with the europium tris- hydroxyethyltriazoledipicolinate complex at 1.51 A resolution.
ComponentsLYSOZYME C
KeywordsHYDROLASE / CLICK-CHEMISTRY / ANOMALOUS SCATTERING / DE NOVO PHASING / LANTHANIDE COMPLEX / DIPICOLINATE
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
ACETATE ION / EUROPIUM (III) ION / Chem-IKX / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.507 Å
AuthorsTalon, R. / Kahn, R. / Gautier, A. / Nauton, L. / Girard, E.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2012
Title: Clicked Europium Dipicolinate Complexes for Protein X-Ray Structure Determination.
Authors: Talon, R. / Nauton, L. / Canet, J.-L. / Kahn, R. / Girard, E. / Gautier, A.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: Protein Crystallography Through Supramolecular Interactions between a Lanthanide Complex and Arginine.
Authors: Pompidor, G. / D'Aleo, A. / Vicat, J. / Toupet, L. / Giraud, N. / Kahn, R. / Maury, O.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: A Dipicolinate Lanthanide Complex for Solving Protein Structures Using Anomalous Diffraction.
Authors: Pompidor, G. / Maury, O. / Vicat, J. / Kahn, R.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Gd-Hpdo3A, a Complex to Obtain High-Phasing-Power Heavy-Atom Derivatives for Sad and MAD Experiments: Results with Tetragonal Hen Egg-White Lysozyme.
Authors: Girard, E. / Chantalat, L. / Vicat, J. / Kahn, R.
History
DepositionSep 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2May 29, 2013Group: Derived calculations
Revision 1.3Apr 1, 2015Group: Database references
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,74817
Polymers14,3311
Non-polymers1,41716
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.763, 77.763, 37.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2065-

HOH

21A-2092-

HOH

31A-2139-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D IV / GAL D 4 / HEWL / MURAMIDASE / MUCOPEPTIDE N- ...1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D IV / GAL D 4 / HEWL / MURAMIDASE / MUCOPEPTIDE N-ACETYLMURAMOYL-HYDROLASE


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ROCHE APPLIED SCIENCE POWDER, CATALOG NUMBER 10837059001
Source: (natural) GALLUS GALLUS (chicken) / Organ: EGG / References: UniProt: P00698, lysozyme

-
Non-polymers , 6 types, 164 molecules

#2: Chemical ChemComp-EU3 / EUROPIUM (III) ION / Europium


Mass: 151.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Eu
#3: Chemical ChemComp-IKX / 4-(4-(2-hydroxyethyl)-1H-1,2,3-triazol-1-yl)pyridine-2,6-dicarboxylic acid


Mass: 280.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N4O5
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE SEQUENCE PROVIDED CORRESPOND TO THE RESIDUES 19 TO 147, I.E WITHOUT THE SIGNAL PEPTIDE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 27 %
Description: MAD DATA AT TWO WAVELENGTHS WERE COLLECTED. THE FIRST DATA SET AT THE EUROPIUM LIII EDGE AND THE SECOND ONE AT THE SELENIUM K EDGE
Crystal growTemperature: 293 K / pH: 4.6
Details: 0.1 M SODIUM ACETATE PH 4.6, 0.4-1.5 M SODIUM CHLORIDE, 0.00046 M PROTEIN, 0.001.4 M LANTHANIDE COMPLEX, 293 K, 3-7 DAYS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 6, 2009 / Details: MIRRORS
RadiationMonochromator: EITHER SI111 OR SI311 CRYSTALS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.51→38.88 Å / Num. obs: 18899 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 13.6 % / Biso Wilson estimate: 13.89 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.3
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.507→31.203 Å / SU ML: 0.29 / σ(F): 1.38 / Phase error: 13.38 / Stereochemistry target values: ML
Details: LIGAND OCCUPANCIES WERE FIXED ACCORDING TO THE ANTHANIDE ION OCCUPANCY
RfactorNum. reflection% reflection
Rfree0.1792 963 5.1 %
Rwork0.1564 --
obs0.1576 18848 99.66 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.575 Å2 / ksol: 0.449 e/Å3
Displacement parametersBiso mean: 15.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.398 Å20 Å20 Å2
2---0.398 Å20 Å2
3---0.796 Å2
Refinement stepCycle: LAST / Resolution: 1.507→31.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 76 148 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111144
X-RAY DIFFRACTIONf_angle_d1.3841553
X-RAY DIFFRACTIONf_dihedral_angle_d26.479445
X-RAY DIFFRACTIONf_chiral_restr0.09154
X-RAY DIFFRACTIONf_plane_restr0.006206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5065-1.5860.21821360.18062447X-RAY DIFFRACTION98
1.586-1.68530.17531370.14562505X-RAY DIFFRACTION100
1.6853-1.81540.15251380.15062527X-RAY DIFFRACTION100
1.8154-1.99810.17911420.14422530X-RAY DIFFRACTION100
1.9981-2.28720.1881480.14372546X-RAY DIFFRACTION100
2.2872-2.88130.18381370.15242592X-RAY DIFFRACTION100
2.8813-31.210.17441250.16712738X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4570.31090.33340.99330.27010.7808-0.0960.01920.1398-0.10840.05050.0634-0.1073-0.03530.0380.112-0.009-0.02410.08610.02110.110120.13865.39724.6033
21.7656-0.0522-0.05421.66080.29031.1295-0.0371-0.2777-0.1520.2102-0.01470.03150.05250.15670.02020.1344-0.0194-0.00880.13060.03340.116615.3194-7.066917.7943
31.9150.130.05480.85530.45920.87020.0004-0.06190.0877-0.00060.00790.03180.0335-0.0042-0.01220.1121-0.0009-0.00240.08580.01790.096323.82712.787411.1114
42.6884-1.54170.96944.5335-1.59622.7783-0.01550.26830.3721-0.28250.01850.0326-0.2958-0.09780.01010.2798-0.0155-0.00920.180.07690.179423.674911.9627-3.9767
50.37570.63240.46541.16530.46041.58780.05320.17330.0232-0.1549-0.06370.02790.11480.0397-0.00340.1426-0.0039-0.00960.17110.00770.056722.77041.346-9.2033
62.20151.7153-1.6323.5974-3.26753.3405-0.10590.8159-1.203-0.1134-0.25681.71010.8869-1.38330.36660.355-0.09870.01240.4006-0.00870.281721.9927-2.958115.4704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:43)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 44:82)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 83:122)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 123:129)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1130:1132)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1133)

+
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