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- PDB-1gzy: Human Insulin-like growth factor; In-house data -

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Basic information

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


glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration ...glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of neuroinflammatory response / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / negative regulation of vascular associated smooth muscle cell apoptotic process / bone mineralization involved in bone maturation / IRS-related events triggered by IGF1R / positive regulation of cell growth involved in cardiac muscle cell development / exocytic vesicle / positive regulation of transcription regulatory region DNA binding / cell activation / positive regulation of calcineurin-NFAT signaling cascade / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of Ras protein signal transduction / myoblast differentiation / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / muscle organ development / negative regulation of interleukin-1 beta production / positive regulation of DNA binding / negative regulation of release of cytochrome c from mitochondria / positive regulation of cardiac muscle hypertrophy / positive regulation of smooth muscle cell migration / positive regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / negative regulation of tumor necrosis factor production / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / SHC-related events triggered by IGF1R / positive regulation of osteoblast differentiation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / activation of protein kinase B activity / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of epithelial cell proliferation / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / insulin receptor binding / growth factor activity / wound healing / regulation of protein phosphorylation / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / integrin binding / Platelet degranulation / response to heat / regulation of gene expression / Ras protein signal transduction / cell population proliferation / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / positive regulation of cell migration / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Insulin-like growth factor I / Insulin-like, subunit E / Insulin-like / 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 growth factor I / Insulin-like, subunit E / Insulin-like / 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 I / Insulin-like growth factor I
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 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
DepositionJun 10, 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 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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 1.5Oct 23, 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

Downloads & links

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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
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.723, 69.282, 64.528
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.: 15 / 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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 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
Highest resolution: 2.54 Å / Lowest resolution: 18 Å / Num. obs: 2065 / % possible obs: 98.1 % / Num. measured all: 8654 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2.54 Å / Lowest resolution: 2.48 Å / % possible obs: 95 % / Rmerge(I) obs: 0.331

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Processing

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

4ins


Resolution: 2.54→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.528 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 1.344 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 198 9.2 %RANDOM
Rwork0.213 ---
obs0.218 1952 88.2 %-
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: 30.68 Å2
Baniso -1Baniso -2Baniso -3
1--3.75 Å20 Å20 Å2
2--1.92 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.54→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms447 0 20 15 482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021462
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.4192.026622
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_restr10.673555
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02339
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.310.2222
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3021.5282
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2082448
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7223180
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5644.5174
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: 2.54→2.68 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.373 14
Rwork0.311 143
Refinement TLS params.Method: refined / Origin x: 10.2011 Å / Origin y: 10.2744 Å / Origin z: 29.3898 Å
111213212223313233
T0.0692 Å2-0.0384 Å20.0555 Å2-0.0224 Å2-0.0255 Å2--0.0707 Å2
L17.2111 °21.005 °2-4.9461 °2-10.5768 °20.3103 °2--10.088 °2
S-0.5984 Å °0.4717 Å °-1.3821 Å °-0.0235 Å °-0.1347 Å °-0.3547 Å °1.2472 Å °-0.1393 Å °0.7331 Å °
Refinement
*PLUS
Lowest resolution: 18 Å / Num. reflection Rfree: 175 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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