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- PDB-5z4w: Crystal structure of signalling protein from buffalo (SPB-40) wit... -

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Basic information

Entry
Database: PDB / ID: 5z4w
TitleCrystal structure of signalling protein from buffalo (SPB-40) with an altered conformation of Trp78 at 1.79 A resolution
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 catabolic process / positive regulation of peptidyl-threonine phosphorylation / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of interleukin-8 production / lung development ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin catabolic process / positive regulation of peptidyl-threonine phosphorylation / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / 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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ETHANOL / Chitinase-3-like protein 1
Similarity search - Component
Biological speciesBubalus bubalis (water buffalo)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSingh, P.K. / Chaudhary, A. / Tyagi, T.K. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Arch. Biochem. Biophys. / Year: 2018
Title: A glycoprotein from mammary gland secreted during involution promotes apoptosis: Structural and biological studies.
Authors: Chaudhary, A. / Kumar, V. / Singh, P.K. / Sharma, P. / Bairagya, H.R. / Kaur, P. / Sharma, S. / Chauhan, S.S. / Singh, T.P.
History
DepositionJan 15, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 14, 2018ID: 5WSM
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_conn / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)41,0964
Polymers40,7111
Non-polymers3853
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-9 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.068, 66.735, 106.072
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 / Mammary gland protein 40 / SPB-40


Mass: 40710.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bubalus bubalis (water buffalo) / References: UniProt: Q7YS85
#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


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


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSequence of this structure is based on reference 1 of database Q7YS85 (CH3L1_BUBBU) in UniProtKB. ...Sequence of this structure is based on reference 1 of database Q7YS85 (CH3L1_BUBBU) in UniProtKB. Residue D232 is missing according to the reference.

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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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 35mM Tris-HCl, 25mM NaCl, 20% ethanol pH 8.0 / PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2013 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.79→56.5 Å / Num. obs: 40939 / % possible obs: 99.6 % / Redundancy: 4.2 % / Rsym value: 0.062 / Net I/σ(I): 2.1
Reflection shellResolution: 1.79→1.84 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q7N

4q7n


Resolution: 1.79→56.49 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.31 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2050 5 %RANDOM
Rwork0.15 ---
obs0.152 38703 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---1.2 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.79→56.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 25 385 3284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192976
X-RAY DIFFRACTIONr_bond_other_d0.0030.022704
X-RAY DIFFRACTIONr_angle_refined_deg2.5291.9444036
X-RAY DIFFRACTIONr_angle_other_deg1.32636249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6355359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54123.214140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98615476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1771520
X-RAY DIFFRACTIONr_chiral_restr0.1840.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02666
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_it1.6161.6211440
X-RAY DIFFRACTIONr_mcbond_other1.6161.6221441
X-RAY DIFFRACTIONr_mcangle_it2.5822.4191797
X-RAY DIFFRACTIONr_mcangle_other2.5842.4211798
X-RAY DIFFRACTIONr_scbond_it2.381.9291536
X-RAY DIFFRACTIONr_scbond_other2.3791.931537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6872.7812240
X-RAY DIFFRACTIONr_long_range_B_refined7.17733.44315577
X-RAY DIFFRACTIONr_long_range_B_other7.17133.36615553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 142 -
Rwork0.245 2574 -
obs--90.44 %
Refinement TLS params.Method: refined / Origin x: 21.7436 Å / Origin y: -2.6351 Å / Origin z: -6.8875 Å
111213212223313233
T0.0082 Å2-0.0066 Å2-0.0074 Å2-0.0298 Å20.0184 Å2--0.0194 Å2
L1.3659 °2-0.1196 °2-0.1939 °2-1.6213 °20.749 °2--1.9691 °2
S-0.0136 Å °0.0647 Å °0.0671 Å °0.0137 Å °0.0172 Å °-0.0965 Å °0.0631 Å °0.1214 Å °-0.0036 Å °

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