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- PDB-1sr0: Crystal structure of signalling protein from sheep(SPS-40) at 3.0... -

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Basic information

Entry
Database: PDB / ID: 1sr0
TitleCrystal structure of signalling protein from sheep(SPS-40) at 3.0A resolution using crystal grown in the presence of polysaccharides
Componentssignal processing protein
KeywordsUNKNOWN FUNCTION / Signalling protein / involution
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 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 speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSrivastava, D.B. / Ethayathulla, A.S. / Singh, N. / Kumar, J. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of signalling protein from sheep(SPS-40) at 3.0A resolution using crystal grown in the presence of polysaccharides
Authors: Srivastava, D.B. / Ethayathulla, A.S. / Singh, N. / Kumar, J. / Sharma, S. / Singh, T.P.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: signal processing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5242
Polymers40,6131
Non-polymers9111
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.793, 66.386, 107.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological Unit is a Monomer

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Components

#1: Protein signal processing protein /


Mass: 40612.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Production host: Escherichia coli (E. coli) / References: GenBank: 37576792, UniProt: Q6TMG6*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-3DManpb1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2-3-3-3/a4-b1_b4-c1_c3-d1_d4-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 25mM tris-HCl,50mM NACl,19% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5412 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 27, 2003 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 3→56 Å / Num. all: 205026 / Num. obs: 7210 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.43 % / Biso Wilson estimate: 36.7 Å2 / Rsym value: 0.133 / Net I/σ(I): 6.8
Reflection shellResolution: 3→3.1 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.523 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OWQ

1owq


Resolution: 3.05→56 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 24.331 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20547 353 4.9 %RANDOM
Rwork0.17231 ---
all0.1747 7210 --
obs0.17403 6857 80 %-
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: 28.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---1.32 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 3.05→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 61 78 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0213009
X-RAY DIFFRACTIONr_bond_other_d0.0030.022629
X-RAY DIFFRACTIONr_angle_refined_deg2.4261.9614094
X-RAY DIFFRACTIONr_angle_other_deg1.71836083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1143359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45715482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1640.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023306
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02655
X-RAY DIFFRACTIONr_nbd_refined0.2940.3883
X-RAY DIFFRACTIONr_nbd_other0.2610.32975
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.6730.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.5210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0620.54
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.322
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0370.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4211.51791
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.66822871
X-RAY DIFFRACTIONr_scbond_it3.38531218
X-RAY DIFFRACTIONr_scangle_it5.6854.51223
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.054→3.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 12
Rwork0.251 376

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