[English] 日本語
Yorodumi
- PDB-1uuz: IVY:A NEW FAMILY OF PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uuz
TitleIVY:A NEW FAMILY OF PROTEIN
Components
  • INHIBITOR OF VERTEBRATE LYSOZYME
  • LYSOZYME C
KeywordsHYDROLASE/INHIBITOR / LYSOZYME-INHIBITOR COMPLEX / IVY / TYPE-C LYSOZYME INHIBITOR / LYSOZYME / HYDROLASE / GLYCOSIDASE / HYDROLASE-INHIBITOR complex
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 / periplasmic space ...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 / periplasmic space / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme superfamily / Inhibitor of vertebrate lysozyme (Ivy) / Inhibitor of vertebrate lysozyme, Ivy / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 ...Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme superfamily / Inhibitor of vertebrate lysozyme (Ivy) / Inhibitor of vertebrate lysozyme, Ivy / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Lysozyme C / Inhibitor of vertebrate lysozyme
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
GALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAbergel, C. / Lembo, F. / Byrne, D. / Maza, C. / Claverie, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structure and Evolution of the Ivy Protein Family, Unexpected Lysozyme Inhibitors in Gram-Negative Bacteria.
Authors: Abergel, C. / Monchois, V. / Byrne, D. / Chenivesse, S. / Lembo, F. / Lazzaroni, J.-C. / Claverie, J.M.
History
DepositionJan 12, 2004Deposition site: PDBE / Processing site: PDBE
SupersessionJan 14, 2004ID: 1HKE
Revision 1.0Jan 14, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INHIBITOR OF VERTEBRATE LYSOZYME
B: INHIBITOR OF VERTEBRATE LYSOZYME
C: LYSOZYME C
D: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)59,7614
Polymers59,7614
Non-polymers00
Water6,954386
1
A: INHIBITOR OF VERTEBRATE LYSOZYME
D: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)29,8802
Polymers29,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: INHIBITOR OF VERTEBRATE LYSOZYME
C: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)29,8802
Polymers29,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.346, 60.760, 78.245
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein INHIBITOR OF VERTEBRATE LYSOZYME / IVY


Mass: 15549.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: IVY COMPLEXED WITH HEWL IN CRYSTAL / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Description: C-TERM HIS-TAG / Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HXB1
#2: Protein LYSOZYME C


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LOOP CKPHDC IS RESPONSIBLE OF THE C-TYPE LYSOZYME ACTIVITY INHIBITION
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growpH: 6.5
Details: 20% POLYETHYLENEGLYCOL 4000, IMIDAZOLE/MALATE 0.2M PH 6.0, 5% GLYCEROL
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.4 mg/mlprotein1drop
220 mMTris1droppH8
30.2 Mimidazole malate1reservoirpH6.0
415-20 %(w/v)PEG40001reservoir
55 %glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→47.673 Å / Num. obs: 42990 / % possible obs: 96.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.3 / % possible all: 96.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 25 Å / Redundancy: 2.8 % / Num. measured all: 122164 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 96.5 % / Redundancy: 2.8 % / Num. unique obs: 4166 / Num. measured obs: 11604 / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPQ

1gpq


Resolution: 1.8→23.94 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4331 10.1 %RANDOM
Rwork0.213 ---
obs0.213 42946 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.456 Å2 / ksol: 0.325439 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å24.45 Å2
2--5.35 Å20 Å2
3----2.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 0 386 4409
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_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 690 9.8 %
Rwork0.27 6382 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 9.9 % / 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_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

+
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