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- PDB-1zb5: Recognition of peptide ligands by signalling protein from porcine... -

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Basic information

Entry
Database: PDB / ID: 1zb5
TitleRecognition of peptide ligands by signalling protein from porcine mammary gland (SPP-40): Crystal structure of the complex of SPP-40 with a peptide Trp-Pro-Trp at 2.45A resolution
Components
  • PEPTIDE TRP-PRO-TRP
  • signal processing protein
KeywordsSIGNALING PROTEIN / PEPTIDIC LIGANDS / SPP-40
Function / homology
Function and homology information


response to interleukin-6 / activation of NF-kappaB-inducing kinase 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 ...response to interleukin-6 / activation of NF-kappaB-inducing kinase 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 / extracellular region / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSrivastava, D.B. / Ethayathulla, A.S. / Kumar, J. / Singh, N. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Kaur, P. / Singh, T.P.
CitationJournal: To be Published
Title: Recognition of peptide ligands by signalling protein from porcine mammary gland (SPP-40): Crystal structure of the complex of SPP-40 with a peptide Trp-Pro-Trp at 2.45A resolution
Authors: Srivastava, D.B. / Ethayathulla, A.S. / Kumar, J. / Singh, N. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Kaur, P. / Singh, T.P.
History
DepositionApr 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: signal processing protein
B: PEPTIDE TRP-PRO-TRP
C: PEPTIDE TRP-PRO-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1014
Polymers41,6773
Non-polymers4241
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.380, 66.790, 107.660
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 signal processing protein


Mass: 40701.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: mammary gland / References: GenBank: 54125563, UniProt: Q29411*PLUS
#2: Protein/peptide PEPTIDE TRP-PRO-TRP


Mass: 487.550 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was synthesized using Trp-Pro-Trp Solid Phase Peptide synthesis. The sequence of the peptide is naturally found in Porcine.
#3: Polysaccharide 2-acetamido-2-deoxy-beta-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
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 56.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 25mM tris-HCl, 11% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 2004 / 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: 2.45→20 Å / Num. all: 17202 / Num. obs: 16643 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.077 / Net I/σ(I): 9.7
Reflection shellResolution: 2.45→2.49 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.412 / % possible all: 96.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1xrv

1xrv


Resolution: 2.45→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 339 -RANDOM
Rwork0.192 ---
all0.194 17202 --
obs0.193 16304 95.2 %-
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20 Å2
2---2.44 Å20 Å2
3---5.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 28 138 3113
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.6
X-RAY DIFFRACTIONr_dihedral_angle_1_deg24.6
X-RAY DIFFRACTIONx_dihedral_angle_d1.11
X-RAY DIFFRACTIONx_mcbond_it1.9981.5
X-RAY DIFFRACTIONx_mcangle_it3.2982
X-RAY DIFFRACTIONx_scbond_it3.1872
X-RAY DIFFRACTIONx_scangle_it4.7112.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.277 62 -
Rwork0.251 --
obs-2680 97.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4carbohydrate.param

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