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- PDB-4mpk: Crystal structure of the complex of buffalo signaling protein SPB... -

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Basic information

Entry
Database: PDB / ID: 4mpk
TitleCrystal structure of the complex of buffalo signaling protein SPB-40 with N-acetylglucosamine at 2.65 A resolution
ComponentsChitinase-3-like protein 1
KeywordsSIGNALING PROTEIN / Text SPB-40 / TIM barrel / N-acetylglucosamine
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 A; domain 3 - #10 / : / 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 / 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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
Chitinase-3-like protein 1
Similarity search - Component
Biological speciesBubalus bubalis (water buffalo)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsYamini, S. / Chaudhary, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the complex of buffalo signaling protein SPB-40 with N-acetylglucosamine at 2.65 A resolution
Authors: Yamini, S. / Chaudhary, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4774
Polymers40,9421
Non-polymers5353
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.938, 67.110, 107.006
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: 40942.238 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.: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 298 K / pH: 8
Details: 25mM Tris, 50mM NaCl, 20% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 19, 2013 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 13282 / % possible obs: 100 % / Observed criterion σ(I): 0 / Rsym value: 0.102 / Net I/σ(I): 17.8
Reflection shellResolution: 2.65→2.7 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.433 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9O

2o9o


Resolution: 2.65→41.61 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 10.222 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 1.435 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 655 4.9 %RANDOM
Rwork0.174 ---
obs0.177 12604 99.8 %-
all-13282 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0 Å2
2---1.09 Å2-0 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.65→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 35 140 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193010
X-RAY DIFFRACTIONr_bond_other_d0.0030.022790
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9434087
X-RAY DIFFRACTIONr_angle_other_deg0.9473.0016376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4122.817142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.44615476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.861523
X-RAY DIFFRACTIONr_chiral_restr0.0970.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023402
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02761
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_it2.1312.3861442
X-RAY DIFFRACTIONr_mcbond_other2.0952.3811441
X-RAY DIFFRACTIONr_mcangle_it3.6653.5661799
X-RAY DIFFRACTIONr_mcangle_other3.6723.571800
X-RAY DIFFRACTIONr_scbond_it2.5572.7821568
X-RAY DIFFRACTIONr_scbond_other2.5562.7821568
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3184.052289
X-RAY DIFFRACTIONr_long_range_B_refined7.25620.523578
X-RAY DIFFRACTIONr_long_range_B_other7.23220.4853553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 52 -
Rwork0.222 873 -
obs--97.88 %

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