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- PDB-1zbk: Recognition of specific peptide sequences by signalling protein f... -

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Basic information

Entry
Database: PDB / ID: 1zbk
TitleRecognition of specific peptide sequences by signalling protein from sheep mammary gland (SPS-40): Crystal structure of the complex of SPS-40 with a peptide Trp-Pro-Trp at 2.9A resolution
Components
  • Chitinase-3 like protein 1
  • PEPTIDE TRP-PRO-TRP
KeywordsSIGNALING PROTEIN / SPS-40 / WPW
Function / homology
Function and homology information


response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / lung development / positive regulation of peptidyl-threonine phosphorylation ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / lung development / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / carbohydrate metabolic process / inflammatory response / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases ...Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chitinase-3-like protein 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSrivastava, D.B. / Ethayathulla, A.S. / Kumar, J. / Singh, N. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Singh, T.P.
CitationJournal: To be Published
Title: Recognition of specific peptide sequences by signalling protein from sheep mammary gland (SPS-40): Crystal structure of the complex of SPS-40 with a peptide Trp-Pro-Trp at 2.9A resolution
Authors: Srivastava, D.B. / Ethayathulla, A.S. / Kumar, J. / Singh, N. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Singh, T.P.
History
DepositionApr 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase-3 like protein 1
C: PEPTIDE TRP-PRO-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5434
Polymers41,1002
Non-polymers4422
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.640, 66.450, 107.440
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 Chitinase-3 like protein 1 / Signal processing protein / Secretory glyoprotein of 40 kDa


Mass: 40612.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Tissue: Mammary glands / References: UniProt: Q6TMG6
#2: Protein/peptide PEPTIDE TRP-PRO-TRP


Mass: 487.550 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED USING Trp-Pro-Trp SOLIDE PHASE PEPTIDE SYNTHESIS
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 25mM tris-HCl, 11% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 14, 2004 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→56 Å / Num. all: 10552 / Num. obs: 9982 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2 / Rsym value: 0.19 / Net I/σ(I): 6.4
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.66 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1r2v

1r2v
PDB Unreleased entry


Resolution: 2.9→56 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 226 -RANDOM
Rwork0.207 ---
all0.209 9982 --
obs0.208 9756 95 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-7.8 Å20 Å20 Å2
2---2.66 Å20 Å2
3----5.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.9→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 30 73 3008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg2.1
X-RAY DIFFRACTIONr_dihedral_angle_1_deg25.8
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.28
LS refinement shellResolution: 2.9→3.07 Å / Rfactor Rfree error: 0.06
RfactorNum. reflection% reflection
Rfree0.37 39 -
Rwork0.33 --
obs-1464 87.7 %

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