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- PDB-5z4v: Crystal structure of the sheep signalling glycoprotein (SPS-40) c... -

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Basic information

Entry
Database: PDB / ID: 5z4v
TitleCrystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40
ComponentsChitinase-3-like protein 1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / 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 insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chitinase-3-like protein 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSharma, P. / Singh, P.K. / Singh, N. / Sharma, S. / Kaur, P. / Betzel, C. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40
Authors: Sharma, P. / Singh, P.K. / Singh, N. / Sharma, S. / Kaur, P. / Betzel, C. / Singh, T.P.
History
DepositionJan 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.d_res_low / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2154
Polymers40,7571
Non-polymers4583
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-24 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.873, 66.415, 105.692
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 / Secretory glycoprotein of 40 kDa / Signal-processing protein


Mass: 40757.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: Q6TMG6
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONFLICTS ARE OBSERVED BETWEEN THE SEQUENCE IN THIS STRUCTURE AND DATABASE UNIPROTKB Q6TMG6 (CH3L1_ ...CONFLICTS ARE OBSERVED BETWEEN THE SEQUENCE IN THIS STRUCTURE AND DATABASE UNIPROTKB Q6TMG6 (CH3L1_SHEEP) THE AUTHOR EXPECTS SEQUENCE IN THIS STRUCTURE TO BE AN ISOFORM. RESIDUE NUMBER 211 IS SIMPLY SKIPPED.

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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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Tri-HCl, 20% Ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2007 / Details: MIRROR
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.65→55.9 Å / Num. obs: 52135 / % possible obs: 99.9 % / Redundancy: 20 % / Rsym value: 0.035 / Net I/σ(I): 13.3
Reflection shellResolution: 1.65→1.68 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PI6

2pi6


Resolution: 1.65→27.711 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.49 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 1075 2.1 %RANDOM
Rwork0.13756 ---
obs0.1385 50989 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.707 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.65→27.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 30 599 3505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0193025
X-RAY DIFFRACTIONr_bond_other_d0.0050.022761
X-RAY DIFFRACTIONr_angle_refined_deg2.8921.9514113
X-RAY DIFFRACTIONr_angle_other_deg1.76336379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04822.917144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78515485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8571524
X-RAY DIFFRACTIONr_chiral_restr0.2040.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213380
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02684
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5561.2661458
X-RAY DIFFRACTIONr_mcbond_other1.5411.2651457
X-RAY DIFFRACTIONr_mcangle_it2.3991.8931824
X-RAY DIFFRACTIONr_mcangle_other2.4011.8941825
X-RAY DIFFRACTIONr_scbond_it2.4321.5431567
X-RAY DIFFRACTIONr_scbond_other2.4311.5441568
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6332.222287
X-RAY DIFFRACTIONr_long_range_B_refined7.29929.09517498
X-RAY DIFFRACTIONr_long_range_B_other7.30129.08617493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.652→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 96 -
Rwork0.178 3688 -
obs--99.4 %
Refinement TLS params.Method: refined / Origin x: -21.7984 Å / Origin y: -2.5073 Å / Origin z: 6.8018 Å
111213212223313233
T0.0011 Å20.0012 Å2-0.0005 Å2-0.0241 Å2-0.0166 Å2--0.0161 Å2
L1.0927 °20.2163 °2-0.0802 °2-1.1468 °2-0.4553 °2--1.4191 °2
S0.0132 Å °-0.0587 Å °0.0441 Å °0.0235 Å °-0.0059 Å °0.0619 Å °0.0024 Å °-0.0802 Å °-0.0073 Å °

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