[English] 日本語
Yorodumi
- PDB-3ulr: Lysozyme contamination facilitates crystallization of a hetero-tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ulr
TitleLysozyme contamination facilitates crystallization of a hetero-trimericCortactin:Arg:Lysozyme complex
Components
  • Abelson tyrosine-protein kinase 2
  • Lysozyme C
  • Src substrate cortactin
KeywordsHYDROLASE / PROTEIN BINDING / SH3 / Protein-protein interaction
Function / homology
Function and homology information


lamellipodium organization / Arp2/3 complex binding / mitotic spindle midzone / regulation of cell projection assembly / Role of ABL in ROBO-SLIT signaling / modification of postsynaptic actin cytoskeleton / regulation of mitophagy / positive regulation of smooth muscle contraction / profilin binding / substrate-dependent cell migration, cell extension ...lamellipodium organization / Arp2/3 complex binding / mitotic spindle midzone / regulation of cell projection assembly / Role of ABL in ROBO-SLIT signaling / modification of postsynaptic actin cytoskeleton / regulation of mitophagy / positive regulation of smooth muscle contraction / profilin binding / substrate-dependent cell migration, cell extension / positive regulation of chemotaxis / regulation of cell motility / focal adhesion assembly / postsynaptic actin cytoskeleton / positive regulation of establishment of T cell polarity / proline-rich region binding / dendritic spine maintenance / podosome / regulation of axon extension / negative regulation of Rho protein signal transduction / cortical cytoskeleton / positive regulation of actin filament polymerization / exploration behavior / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / neuron projection morphogenesis / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / ruffle / clathrin-coated pit / phosphotyrosine residue binding / voltage-gated potassium channel complex / RAC1 GTPase cycle / Negative regulation of FLT3 / receptor-mediated endocytosis / Lactose synthesis / Antimicrobial peptides / peptidyl-tyrosine phosphorylation / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / negative regulation of extrinsic apoptotic signaling pathway / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / actin filament / non-specific protein-tyrosine kinase / intracellular protein transport / enzyme activator activity / cell motility / positive regulation of neuron projection development / protein modification process / epidermal growth factor receptor signaling pathway / cell wall macromolecule catabolic process / actin filament binding / lysozyme / cell junction / lysozyme activity / lamellipodium / actin cytoskeleton / manganese ion binding / positive regulation of cytosolic calcium ion concentration / growth cone / actin cytoskeleton organization / cellular response to oxidative stress / protein tyrosine kinase activity / cell cortex / phospholipase C-activating G protein-coupled receptor signaling pathway / defense response to Gram-negative bacterium / killing of cells of another organism / dendritic spine / protein kinase activity / cell adhesion / defense response to Gram-positive bacterium / regulation of autophagy / defense response to bacterium / focal adhesion / glutamatergic synapse / enzyme binding / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Hs1/Cortactin / Repeat in HS1/Cortactin / Cortactin repeat profile. / Cortactin, SH3 domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Variant SH3 domain / SH3 Domains ...Hs1/Cortactin / Repeat in HS1/Cortactin / Cortactin repeat profile. / Cortactin, SH3 domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Variant SH3 domain / SH3 Domains / : / Lysozyme - #10 / SH3 domain / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Lysozyme / Src homology 3 (SH3) domain profile. / SH3 domain / Lysozyme-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C / Tyrosine-protein kinase ABL2 / Src substrate cortactin
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLiu, W. / MacGrath, S. / Koleske, A.J. / Boggon, T.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Lysozyme contamination facilitates crystallization of a heterotrimeric cortactin-Arg-lysozyme complex.
Authors: Liu, W. / Macgrath, S.M. / Koleske, A.J. / Boggon, T.J.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysozyme C
B: Src substrate cortactin
C: Abelson tyrosine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)23,4033
Polymers23,4033
Non-polymers00
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-12 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.658, 57.838, 95.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: American Bioanalytical AB01178 / Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / References: UniProt: P00698, lysozyme
#2: Protein Src substrate cortactin


Mass: 7202.915 Da / Num. of mol.: 1 / Fragment: SH3 domain (UNP residues 487-546)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 / References: UniProt: Q60598
#3: Protein/peptide Abelson tyrosine-protein kinase 2 / Abelson murine leukemia viral oncogene homolog 2 / Abelson-related gene protein / Tyrosine-protein kinase ARG


Mass: 1869.252 Da / Num. of mol.: 1 / Fragment: PXXP1 (UNP residues 563-579) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42684
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.0M Na Citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2010
Details: Si(111) channel cut monochromator Toroidal focusing mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 25122 / Num. obs: 23866 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.087 / Net I/σ(I): 14.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1704 / Rsym value: 0.35 / % possible all: 65.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D1X and 3M3U

2d1x

3m3u


Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.478 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R Free: 0.11 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22487 1277 5.1 %RANDOM
Rwork0.18426 ---
obs0.18641 22290 94.27 %-
all-23655 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.167 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--3.48 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 0 292 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221672
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9312279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40123.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70515265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8011516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211301
X-RAY DIFFRACTIONr_mcbond_it1.1381.51032
X-RAY DIFFRACTIONr_mcangle_it1.91221653
X-RAY DIFFRACTIONr_scbond_it2.8283640
X-RAY DIFFRACTIONr_scangle_it4.2044.5621
LS refinement shellResolution: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 53 -
Rwork0.322 1080 -
obs--58.95 %

+
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