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- PDB-1ljy: Crystal Structure of a Novel Regulatory 40 kDa Mammary Gland Prot... -

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Basic information

Entry
Database: PDB / ID: 1ljy
TitleCrystal Structure of a Novel Regulatory 40 kDa Mammary Gland Protein (MGP-40) secreted during Involution
ComponentsMGP-40
KeywordsSIGNALING PROTEIN / Mammary Gland protein / Marker protein / Cancer regressor protein
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: 2.9 Å
AuthorsMohanty, A.K. / Singh, G. / Paramasivam, M. / Saravanan, K. / Jabeen, T. / Sharma, S. / Yadav, S. / Kaur, P. / Kumar, P. / Srinivasan, A. / Singh, T.P.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of a Novel Regulatory 40 kDa Mammary Gland Protein (MGP-40) secreted during Involution
Authors: Mohanty, A.K. / Singh, G. / Paramasivam, M. / Saravanan, K. / Jabeen, T. / Sharma, S. / Yadav, S. / Kaur, P. / Kumar, P. / Srinivasan, A. / Singh, T.P.
History
DepositionApr 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MGP-40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0102
Polymers40,5861
Non-polymers4241
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.950, 65.890, 107.030
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 MGP-40


Mass: 40585.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Mammary Gland secretory protein. / Source: (natural) Capra hircus (goat) / References: GenBank: 19526603, UniProt: Q8SPQ0*PLUS
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 8.5
Details: 12%Ethanol, 25 mMTris-HCl, pH 8.5, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein11
210 mMTris-HCl11
319 %(v/v)ethanol12pH8.0

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 26, 2001
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→19.73 Å / Num. all: 10394 / Num. obs: 10394 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Redundancy: 5.49 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.114 / Net I/σ(I): 7
Reflection shellResolution: 2.9→3 Å / % possible all: 99
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.114
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→19.73 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1103275.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 542 5.3 %RANDOM
Rwork0.181 ---
obs0.18 10236 99.2 %-
all-10394 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.07 Å2 / ksol: 0.282382 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2--0.19 Å20 Å2
3---2.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.3 Å
Luzzati d res low-4 Å
Luzzati sigma a0.54 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 28 48 2942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.9
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 81 4.9 %
Rwork0.277 1577 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.9

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