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- PDB-3zxc: E69 deletion mutant single insulin-like growth factor binding dom... -

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Basic information

Entry
Database: PDB / ID: 3zxc
TitleE69 deletion mutant single insulin-like growth factor binding domain protein (SIBD-1) from Cupiennius salei
ComponentsSINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1
KeywordsSIGNALING / IGFBP / SINGLE INSULIN-BINDING DOMAIN
Function / homology
Function and homology information


insulin-like growth factor binding / regulation of signal transduction / regulation of cell growth / innate immune response / extracellular region
Similarity search - Function
Insulin-like growth factor binding protein-related protein (IGFBP-rP), MAC25 / Omega-AgatoxinV - #20 / Omega-AgatoxinV / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Growth factor receptor cysteine-rich domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
ACETATE ION / Single insulin-like growth factor-binding domain protein-1
Similarity search - Component
Biological speciesCUPIENNIUS SALEI (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsWidmer, C. / Baumann, U.
CitationJournal: Proteins / Year: 2012
Title: Structural and Biochemical Characterization of Native and Recombinant Single Insulin-Like Growth Factor-Binding Domain Protein (Sibd-1) from the Central American Hunting Spider Cupiennius Salei (Ctenidae).
Authors: Trachsel, C. / Widmer, C. / Kampfer, U. / Buhr, C. / Baumann, T. / Kuhn-Nentwig, L. / Schurch, S. / Schaller, J. / Baumann, U.
History
DepositionAug 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 2.0Nov 20, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1
B: SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1944
Polymers16,0762
Non-polymers1182
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-24.6 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.460, 49.460, 121.499
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1 / E69 DELETION MUTANT / SIBD-1


Mass: 8038.088 Da / Num. of mol.: 2
Fragment: INSULIN-LIKE GROWTH FACTOR BINDING DOMAIN RESIDUES 20-97
Source method: isolated from a genetically manipulated source
Details: E69 DELETION MUTANT / Source: (gene. exp.) CUPIENNIUS SALEI (spider) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4V4F9
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.91 % / Description: NONE
Crystal growpH: 4.6 / Details: 2.2 M SODIUM CHLORIDE, 0.1M SODIUM ACETATE, PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 34438 / % possible obs: 98.6 % / Observed criterion σ(I): 2.16 / Redundancy: 5.7 % / Biso Wilson estimate: 17.76 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 2.16 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.4→35.007 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 19.31 / Stereochemistry target values: ML
Details: RESIDUES 61-66 IN CHAIN A, 64-67 IN CHAIN B ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.191 1722 5 %
Rwork0.1594 --
obs0.161 34397 98.83 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.16 Å2 / ksol: 0.457 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5121 Å20 Å20 Å2
2--1.5121 Å20 Å2
3----3.0242 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 8 242 1286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081082
X-RAY DIFFRACTIONf_angle_d1.1181454
X-RAY DIFFRACTIONf_dihedral_angle_d21.059663
X-RAY DIFFRACTIONf_chiral_restr0.061152
X-RAY DIFFRACTIONf_plane_restr0.006200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.44120.3081360.25272585X-RAY DIFFRACTION96
1.4412-1.48770.25481430.212716X-RAY DIFFRACTION100
1.4877-1.54090.20251430.17442707X-RAY DIFFRACTION100
1.5409-1.60260.21041430.1562707X-RAY DIFFRACTION100
1.6026-1.67550.20131420.14442689X-RAY DIFFRACTION100
1.6755-1.76390.19831440.142744X-RAY DIFFRACTION100
1.7639-1.87440.20311440.1462733X-RAY DIFFRACTION100
1.8744-2.01910.18051440.14492726X-RAY DIFFRACTION100
2.0191-2.22220.18851450.14422766X-RAY DIFFRACTION100
2.2222-2.54370.21321460.15742756X-RAY DIFFRACTION100
2.5437-3.20450.18811480.16032826X-RAY DIFFRACTION100
3.2045-35.01770.16811440.16422720X-RAY DIFFRACTION92

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