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- PDB-3ulr: Lysozyme contamination facilitates crystallization of a hetero-tr... -

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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 / mitotic spindle midzone / positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of mitophagy / profilin binding / positive regulation of smooth muscle contraction / substrate-dependent cell migration, cell extension / regulation of cell motility / positive regulation of establishment of T cell polarity ...lamellipodium organization / mitotic spindle midzone / positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of mitophagy / profilin binding / positive regulation of smooth muscle contraction / substrate-dependent cell migration, cell extension / regulation of cell motility / positive regulation of establishment of T cell polarity / focal adhesion assembly / dendritic spine maintenance / podosome / exploration behavior / regulation of axon extension / positive regulation of actin filament polymerization / negative regulation of Rho protein signal transduction / cortical cytoskeleton / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / cellular response to retinoic acid / clathrin-coated pit / extrinsic apoptotic signaling pathway / ruffle / voltage-gated potassium channel complex / RAC1 GTPase cycle / phosphotyrosine residue binding / Negative regulation of FLT3 / receptor-mediated endocytosis / neuron projection morphogenesis / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / negative regulation of extrinsic apoptotic signaling pathway / actin filament / non-membrane spanning protein tyrosine kinase activity / regulation of actin cytoskeleton organization / intracellular protein transport / beta-N-acetylglucosaminidase activity / non-specific protein-tyrosine kinase / cell motility / peptidyl-tyrosine phosphorylation / protein modification process / positive regulation of neuron projection development / epidermal growth factor receptor signaling pathway / actin filament binding / cell wall macromolecule catabolic process / cell junction / lysozyme / lysozyme activity / lamellipodium / actin cytoskeleton / manganese ion binding / actin cytoskeleton organization / positive regulation of cytosolic calcium ion concentration / cell cortex / protein tyrosine kinase activity / defense response to Gram-negative bacterium / phospholipase C-activating G protein-coupled receptor signaling pathway / killing of cells of another organism / dendritic spine / protein kinase activity / defense response to Gram-positive bacterium / regulation of autophagy / cell adhesion / defense response to bacterium / focal adhesion / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
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 / : / SH3 domain / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Lysozyme / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 %

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