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- PDB-1gzr: Human Insulin-like growth factor; ESRF data -

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Basic information

Entry
Database: PDB / ID: 1gzr
TitleHuman Insulin-like growth factor; ESRF data
ComponentsINSULIN-LIKE GROWTH FACTOR I
KeywordsGROWTH FACTOR / INSULIN FAMILY / IGF-1 / PLASMA
Function / homology
Function and homology information


prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / type II pneumocyte differentiation / neuronal dense core vesicle lumen / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / regulation of establishment or maintenance of cell polarity ...prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / type II pneumocyte differentiation / neuronal dense core vesicle lumen / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / regulation of establishment or maintenance of cell polarity / positive regulation of trophectodermal cell proliferation / positive regulation of glycoprotein biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / proteoglycan biosynthetic process / myotube cell development / positive regulation of transcription regulatory region DNA binding / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of neuroinflammatory response / lung vasculature development / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / bone mineralization involved in bone maturation / positive regulation of cell growth involved in cardiac muscle cell development / IRS-related events triggered by IGF1R / cerebellar granule cell precursor proliferation / negative regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of myoblast proliferation / exocytic vesicle / lung lobe morphogenesis / positive regulation of myelination / negative regulation of androgen receptor signaling pathway / glial cell differentiation / cell activation / prostate gland growth / positive regulation of calcineurin-NFAT signaling cascade / type B pancreatic cell proliferation / transmembrane receptor protein tyrosine kinase activator activity / mammary gland development / exocrine pancreas development / alphav-beta3 integrin-IGF-1-IGF1R complex / regulation of nitric oxide biosynthetic process / myoblast differentiation / cell surface receptor signaling pathway via STAT / positive regulation of Ras protein signal transduction / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of smooth muscle cell migration / growth hormone receptor signaling pathway / positive regulation of DNA binding / negative regulation of interleukin-1 beta production / lung alveolus development / cellular response to insulin-like growth factor stimulus / muscle organ development / branching morphogenesis of an epithelial tube / positive regulation of cardiac muscle hypertrophy / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / type I pneumocyte differentiation / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / positive regulation of activated T cell proliferation / inner ear development / androgen receptor signaling pathway / myoblast proliferation / blood vessel remodeling / negative regulation of tumor necrosis factor production / epithelial to mesenchymal transition / Synthesis, secretion, and deacylation of Ghrelin / activation of protein kinase B activity / positive regulation of glycogen biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of osteoblast differentiation / SHC-related events triggered by IGF1R / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / positive regulation of epithelial cell proliferation / platelet alpha granule lumen / positive regulation of glycolytic process / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of smooth muscle cell proliferation / cellular response to glucose stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / growth factor activity / wound healing / hormone activity / negative regulation of ERK1 and ERK2 cascade / multicellular organism growth / circadian rhythm / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of fibroblast proliferation / cellular response to amyloid-beta / osteoblast differentiation / integrin binding / insulin receptor signaling pathway
Similarity search - Function
Insulin-like, subunit E / Insulin-like / Insulin-like growth factor I / Insulin-like growth factor / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. ...Insulin-like, subunit E / Insulin-like / Insulin-like growth factor I / Insulin-like growth factor / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C15 / Insulin-like growth factor 1 / Insulin-like growth factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrzozowski, A.M. / Dodson, E.J. / Dodson, G.G. / Murshudov, G. / Verma, C. / Turkenburg, J.P. / De Bree, F.M. / Dauter, Z.
CitationJournal: Biochemistry / Year: 2002
Title: Structural Origins of the Functional Divergence of Human Insulin-Like Growth Factor-I and Insulin
Authors: Brzozowski, A.M. / Dodson, E.J. / Dodson, G.G. / Murshudov, G. / Verma, C. / Turkenburg, J.P. / De Bree, F.M. / Dauter, Z.
History
DepositionMay 28, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 29, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: INSULIN-LIKE GROWTH FACTOR I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0002
Polymers7,6641
Non-polymers3371
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.777, 69.468, 65.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein INSULIN-LIKE GROWTH FACTOR I / SOMATOMEDIN C / IGF1 / IBP1


Mass: 7663.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01343, UniProt: P05019*PLUS
#2: Chemical ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H38NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINSULIN-LIKE GROWTH FACTORS,ARE FUNCTIONALLY AND STRUCTURALLY RELATED TO INSULIN WITH HIGHER GROWTH- ...INSULIN-LIKE GROWTH FACTORS,ARE FUNCTIONALLY AND STRUCTURALLY RELATED TO INSULIN WITH HIGHER GROWTH-PROMOTING ACTIVITY.
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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7. ...Details: THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7.5, 12-15% (W/V) PEG 2K AND 5MM SB12 DETERGENT.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1dropin water
20.1 MTris-HCl1reservoirpH7.5
312-15 %(w/v)PEG2000MME1reservoir
45 mMSB12 detergent1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 4839 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 18
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 12 / % possible all: 95.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 17172
Reflection shell
*PLUS
% possible obs: 95.8 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB EBTRY 4INS

4ins


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.553 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.295 219 4.5 %RANDOM
Rwork0.237 ---
obs0.24 4620 98 %-
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: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å20 Å2
2---1.14 Å20 Å2
3---3 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms470 0 20 30 520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021494
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.5882.027662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr8.17559
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02364
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.280.2178
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3120.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3580.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5691.5302
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2982479
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5323192
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3924.5183
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.11 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.305 37
Rwork0.272 645
Refinement TLS params.Method: refined / Origin x: 10.3522 Å / Origin y: 9.5208 Å / Origin z: 29.3075 Å
111213212223313233
T0.0005 Å2-0.002 Å20.0056 Å2-0.0552 Å2-0.0328 Å2--0.0625 Å2
L7.0382 °2-1.2923 °2-1.1538 °2-9.8523 °2-0.1269 °2--4.952 °2
S-0.2194 Å °0.3002 Å °-0.385 Å °-0.1244 Å °-0.1088 Å °-0.2428 Å °0.353 Å °0.0491 Å °0.3282 Å °
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 208 / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.6

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