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- PDB-1jnd: Crystal structure of imaginal disc growth factor-2 -

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Basic information

Entry
Database: PDB / ID: 1jnd
TitleCrystal structure of imaginal disc growth factor-2
ComponentsImaginal disc growth factor-2
KeywordsHORMONE/GROWTH FACTOR / IDGF / imaginal disc / growth factor / chitinase / insulin receptor / heparin / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


imaginal disc growth factor receptor binding / imaginal disc development / Neutrophil degranulation / chitin catabolic process / chitin binding / carbohydrate metabolic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular region
Similarity search - Function
Imaginal disc growth factor / Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 ...Imaginal disc growth factor / Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / 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-like protein Idgf2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVarela, P.F. / Llera, A.S. / Mariuzza, R.A. / Tormo, J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of imaginal disc growth factor-2. A member of a new family of growth-promoting glycoproteins from Drosophila melanogaster.
Authors: Varela, P.F. / Llera, A.S. / Mariuzza, R.A. / Tormo, J.
History
DepositionJul 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: 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 / 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_struct_special_symmetry / 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_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 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 2.2Nov 13, 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: Imaginal disc growth factor-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7012
Polymers46,9531
Non-polymers7491
Water12,611700
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.345, 106.345, 89.987
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1701-

HOH

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Components

#1: Protein Imaginal disc growth factor-2


Mass: 46952.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: 4092089, UniProt: Q9V3D4*PLUS
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein11
212 %PEG400012
30.1 Msodium acetate12pH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9464 / Wavelength: 0.9464 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. obs: 129904 / % possible obs: 90.3 % / Redundancy: 1.1 % / Rsym value: 0.023
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 1.76 % / Mean I/σ(I) obs: 2.88 / Rsym value: 0.257 / % possible all: 53.5
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 758311 / Rmerge(I) obs: 0.023
Reflection shell
*PLUS
% possible obs: 53.5 % / Rmerge(I) obs: 0.257

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CTN

1ctn


Resolution: 1.3→100 Å / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.202 2298 -
Rwork0.176 --
obs0.176 127327 98.2 %
all-127327 -
Refinement stepCycle: LAST / Resolution: 1.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 50 700 3916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d1.6
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / % reflection Rfree: 1.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.6

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