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- PDB-1lcv: streptavidin-norbiotin complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1lcv
Titlestreptavidin-norbiotin complex
Componentsstreptavidin
KeywordsUNKNOWN FUNCTION / avidin / streptavidin / biotin / biotin-analogues
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
NORBIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLivnah, O. / Pazy, Y.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Ligand exchange between proteins: exchange of biotin and biotin derivatives between avidin and streptavidin
Authors: Pazy, Y. / Kulik, T. / Bayer, E.A. / Wilchek, M. / Livnah, O.
History
DepositionApr 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)25,9904
Polymers25,5302
Non-polymers4612
Water1,69394
1
A: streptavidin
B: streptavidin
hetero molecules

A: streptavidin
B: streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9808
Polymers51,0594
Non-polymers9214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area11350 Å2
ΔGint-75 kcal/mol
Surface area18900 Å2
MethodPISA
2
A: streptavidin
B: streptavidin
hetero molecules

A: streptavidin
B: streptavidin
hetero molecules

A: streptavidin
B: streptavidin
hetero molecules

A: streptavidin
B: streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,96116
Polymers102,1198
Non-polymers1,8428
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)47.290, 95.320, 105.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe second part of the biological assembly is generated by the two fold axis: -x,y -z

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Components

#1: Protein streptavidin


Mass: 12764.833 Da / Num. of mol.: 2
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-SNR / NORBIOTIN / 4-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-4-YL)-BUTYRIC ACID


Mass: 230.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.2 M ammonium sulfate, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.2 mg/mlprotein1drop
212 %PEG10001reservoir
30.1 Mimidazole-malate1reservoirpH5.8

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1999 / Details: short supper mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 10095 / % possible obs: 92.2 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.38 Å / % possible all: 93.4
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 2 % / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 93.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.233 483 random
Rwork0.188 --
all-9526 -
obs-9043 -
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 30 94 1910
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.26

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