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- PDB-2b31: Crystal structure of the complex formed between goat signalling p... -

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Basic information

Entry
Database: PDB / ID: 2b31
TitleCrystal structure of the complex formed between goat signalling protein with pentasaccharide at 3.1 A resolution reveals large scale conformational changes in the residues of TIM barrel
ComponentsChitinase-3-like protein 1, SPG-40
KeywordsSIGNALING PROTEIN / SIGNALLING PROTEIN / COMPLEX PENTASACCHARIDE
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 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production ...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 / 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 / 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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily ...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 speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEthayathulla, A.S. / Kumar, J. / Srivastava, D.B. / Singh, N. / Sharma, S. / Bhushan, A. / Singh, T.P.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the complex formed between goat signalling protein with pentasaccharide at 3.1 A resolution reveals large scale conformational changes in the residues of TIM barrel
Authors: Ethayathulla, A.S. / Kumar, J. / Srivastava, D.B. / Singh, N. / Sharma, S. / Bhushan, A. / Singh, T.P.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionSep 27, 2005ID: 1ZU9
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 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
Remark 999SEQUENCE The authors state that the aminoacid sequence in the database is incorrect for residues ...SEQUENCE The authors state that the aminoacid sequence in the database is incorrect for residues 54, 152, 226, 227 and 382. The authors state that residue 232 should be deleted from the sequence database reference.

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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, SPG-40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1863
Polymers40,7281
Non-polymers1,4582
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.745, 66.613, 107.812
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, SPG-40 / Mammary gland protein MGP-40 / BP40


Mass: 40728.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / Secretion: Mammary gland / References: GenBank: 19526603, UniProt: Q8SPQ0*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAca1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 56.3 %
Crystal growTemperature: 298 K / pH: 7.8
Details: 25mM Tris HCl, 50mM NaCl, 19% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0 K, pH 7.80

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 2005 / 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: 3.1→56.7 Å / Num. obs: 8493 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Rsym value: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 3.1→3.21 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.43 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZO

1qzo
PDB Unreleased entry


Resolution: 3.1→56.7 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 25.315 / SU ML: 0.464 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21782 403 4.7 %RANDOM
Rwork0.1766 ---
obs0.17859 8090 98.17 %-
all-8493 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.973 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 3.1→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 98 71 3045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213057
X-RAY DIFFRACTIONr_bond_other_d0.0030.022703
X-RAY DIFFRACTIONr_angle_refined_deg2.441.9724152
X-RAY DIFFRACTIONr_angle_other_deg2.38136234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2433359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.79315497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1520.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023334
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02671
X-RAY DIFFRACTIONr_nbd_refined0.2960.3744
X-RAY DIFFRACTIONr_nbd_other0.2680.32855
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.4720.510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.5165
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2310.55
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4090.319
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6831.51791
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.16322872
X-RAY DIFFRACTIONr_scbond_it3.41731266
X-RAY DIFFRACTIONr_scangle_it5.6344.51280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 30
Rwork0.243 609

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