[English] 日本語
Yorodumi
- PDB-4phi: Crystal structure of HEWL with hexatungstotellurate(VI) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4phi
TitleCrystal structure of HEWL with hexatungstotellurate(VI)
ComponentsLysozyme C
KeywordsHYDROLASE / polyoxometalate / Anderson Evans type
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / 6-tungstotellurate(VI) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.811 Å
AuthorsBijelic, A. / Molitor, C. / Mauracher, S.G. / Al-Oweini, R. / Kortz, U. / Rompel, A.
CitationJournal: Chembiochem / Year: 2015
Title: Hen Egg-White Lysozyme Crystallisation: Protein Stacking and Structure Stability Enhanced by a Tellurium(VI)-Centred Polyoxotungstate.
Authors: Bijelic, A. / Molitor, C. / Mauracher, S.G. / Al-Oweini, R. / Kortz, U. / Rompel, A.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 2.0Nov 6, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
C: Lysozyme C
D: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,59021
Polymers57,3254
Non-polymers13,26517
Water11,638646
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7356
Polymers14,3311
Non-polymers3,4035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-54 kcal/mol
Surface area22420 Å2
MethodPISA
3
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4508
Polymers14,3311
Non-polymers8,1197
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3773
Polymers14,3311
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0284
Polymers14,3311
Non-polymers1,6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.010, 60.010, 261.840
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
11C-302-

HOH

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 14331.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

-
Non-polymers , 5 types, 663 molecules

#2: Chemical
ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O24TeW6
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.2 M sodium chloride, 0.1 M sodium acetate pH 4.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0207 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0207 Å / Relative weight: 1
ReflectionResolution: 1.811→29.25 Å / Num. obs: 80356 / % possible obs: 99.99 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / Net I/σ(I): 15.72
Reflection shellResolution: 1.81→1.859 Å / Redundancy: 17.8 % / Rmerge(I) obs: 1.702 / Num. measured obs: 80356 / Num. unique all: 4520 / Rsym value: 1.7 / % possible all: 99.89

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.811→29.247 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 4149 4.99 %
Rwork0.187 --
obs0.1876 83164 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.811→29.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 268 646 4782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034311
X-RAY DIFFRACTIONf_angle_d0.7176388
X-RAY DIFFRACTIONf_dihedral_angle_d11.2091381
X-RAY DIFFRACTIONf_chiral_restr0.025563
X-RAY DIFFRACTIONf_plane_restr0.002696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8105-1.83110.30151340.2592591X-RAY DIFFRACTION100
1.8311-1.85260.25691390.2542630X-RAY DIFFRACTION100
1.8526-1.87520.25481390.25222707X-RAY DIFFRACTION100
1.8752-1.89890.22541350.24392579X-RAY DIFFRACTION100
1.8989-1.92390.24381380.24652655X-RAY DIFFRACTION100
1.9239-1.95030.24541400.23872632X-RAY DIFFRACTION100
1.9503-1.97810.21821370.22712629X-RAY DIFFRACTION100
1.9781-2.00760.25751340.22832640X-RAY DIFFRACTION100
2.0076-2.0390.22051390.21632600X-RAY DIFFRACTION100
2.039-2.07240.19421460.2192708X-RAY DIFFRACTION100
2.0724-2.10820.25421360.21392557X-RAY DIFFRACTION100
2.1082-2.14650.251410.21222664X-RAY DIFFRACTION100
2.1465-2.18770.21891450.21682628X-RAY DIFFRACTION100
2.1877-2.23240.24591380.20442655X-RAY DIFFRACTION100
2.2324-2.28090.24161360.20492610X-RAY DIFFRACTION100
2.2809-2.33390.21531370.20492609X-RAY DIFFRACTION100
2.3339-2.39230.23121400.19092676X-RAY DIFFRACTION100
2.3923-2.45690.20961380.20062601X-RAY DIFFRACTION100
2.4569-2.52920.18071390.19872649X-RAY DIFFRACTION100
2.5292-2.61080.19191440.1912659X-RAY DIFFRACTION100
2.6108-2.7040.18041430.18432609X-RAY DIFFRACTION100
2.704-2.81220.17661340.17932630X-RAY DIFFRACTION100
2.8122-2.94010.18921340.16792635X-RAY DIFFRACTION100
2.9401-3.09490.19881350.1752648X-RAY DIFFRACTION100
3.0949-3.28860.1871410.16342627X-RAY DIFFRACTION100
3.2886-3.54210.15891410.15632657X-RAY DIFFRACTION100
3.5421-3.89780.18891330.15912616X-RAY DIFFRACTION100
3.8978-4.46020.15281430.14282635X-RAY DIFFRACTION100
4.4602-5.61280.15941320.16922641X-RAY DIFFRACTION100
5.6128-29.25050.22161380.1952638X-RAY DIFFRACTION100

+
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