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- PDB-1i9h: CORE STREPTAVIDIN-BNA COMPLEX -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1i9h
TitleCORE STREPTAVIDIN-BNA COMPLEX
ComponentsSTREPTAVIDIN
KeywordsUNKNOWN FUNCTION / classical beta barrel / protein-ligand complex
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BNI / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLivnah, O. / Huberman, T. / Wilchek, M. / Bayer, E.A. / Eisenberg-Domovich, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Chicken avidin exhibits pseudo-catalytic properties. Biochemical, structural, and electrostatic consequences.
Authors: Huberman, T. / Eisenberg-Domovich, Y. / Gitlin, G. / Kulik, T. / Bayer, E.A. / Wilchek, M. / Livnah, O.
History
DepositionMar 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7244
Polymers28,9952
Non-polymers7292
Water2,414134
1
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4488
Polymers57,9914
Non-polymers1,4584
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)47.121, 95.160, 105.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein STREPTAVIDIN


Mass: 14497.639 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-BNI / 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE / BIOTINYL P-NITROANILINE


Mass: 364.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N4O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% isopropanol, 0.1M NaCitrate, 0.05M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Msodium citrate1reservoir
20.1 MHEPES1reservoir
320 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 20, 1998 / Details: short Supper Mirrors
RadiationMonochromator: Chales Supper short mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 8647 / Num. obs: 8647 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2 % / Rmerge(I) obs: 0.265 / % possible all: 94.2
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 2 %
Reflection shell
*PLUS
% possible obs: 94.2 % / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZF

2izf


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 454 5 %random
Rwork0.1773 ---
all0.1812 9609 --
obs0.1812 8379 --
Solvent computationksol: 0.335388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.435 Å20 Å20 Å2
2--0.679 Å20 Å2
3---3.756 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 50 134 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1861.5
X-RAY DIFFRACTIONc_mcangle_it2.0352
X-RAY DIFFRACTIONc_scbond_it1.5172
X-RAY DIFFRACTIONc_scangle_it2.2982.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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