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- PDB-4dne: Crystal structure of a triple-mutant of streptavidin in complex w... -

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Basic information

Entry
Database: PDB / ID: 4dne
TitleCrystal structure of a triple-mutant of streptavidin in complex with desthiobiotin
ComponentsStreptavidin
KeywordsBIOTIN-BINDING PROTEIN / biotin
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-DTB / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsPanwar, P. / Deniaud, A. / Pebay-Peyroula, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Contamination from an affinity column: an encounter with a new villain in the world of membrane-protein crystallization.
Authors: Panwar, P. / Deniaud, A. / Pebay-Peyroula, E.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Apr 6, 2016Group: Non-polymer description
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)38,78810
Polymers37,7842
Non-polymers1,0058
Water1,63991
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,57720
Polymers75,5674
Non-polymers2,01016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area14500 Å2
ΔGint-271 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.720, 93.782, 104.413
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: 18891.777 Da / Num. of mol.: 2 / Mutation: E44V, S45T, V47R
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-DTB / 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID / D-DESTHIOBIOTIN


Mass: 214.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM MgSO4, 50 mM Na caodylate, 2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 4, 2009
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 19193 / Num. obs: 19097 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.121
Reflection shellResolution: 1.88→1.98 Å / Rmerge(I) obs: 0.41 / % possible all: 96.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MERLOTphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MK5

1mk5


Resolution: 1.88→46.86 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.817 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21897 966 5.1 %RANDOM
Rwork0.18141 ---
all0.18323 18230 --
obs0.18323 18119 99.39 %-
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: 15.225 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 60 91 1960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211953
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9212680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9355249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.77422.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37115261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8991512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021488
X-RAY DIFFRACTIONr_mcbond_it0.7651.51195
X-RAY DIFFRACTIONr_mcangle_it1.39721906
X-RAY DIFFRACTIONr_scbond_it1.8573758
X-RAY DIFFRACTIONr_scangle_it2.7824.5771
LS refinement shellResolution: 1.88→1.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 70 -
Rwork0.235 1210 -
obs--93.57 %

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