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- PDB-3szh: Crystal structure of apo shwanavidin (P1 form) -

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Basic information

Entry
Database: PDB / ID: 3szh
TitleCrystal structure of apo shwanavidin (P1 form)
ComponentsAvidin/streptavidin
KeywordsBiotin-binding protein / high affinity systems / avidin / streptavidin / biotin / shwanavidin
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesShewanella denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsLivnah, O. / Meir, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Adaptation of a Thermostable Biotin-binding Protein in a Psychrophilic Environment.
Authors: Meir, A. / Bayer, E.A. / Livnah, O.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 13, 2012Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avidin/streptavidin
B: Avidin/streptavidin
C: Avidin/streptavidin
D: Avidin/streptavidin
E: Avidin/streptavidin
F: Avidin/streptavidin


Theoretical massNumber of molelcules
Total (without water)78,2186
Polymers78,2186
Non-polymers00
Water15,331851
1
A: Avidin/streptavidin
B: Avidin/streptavidin


Theoretical massNumber of molelcules
Total (without water)26,0732
Polymers26,0732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-22 kcal/mol
Surface area9840 Å2
MethodPISA
2
C: Avidin/streptavidin
D: Avidin/streptavidin


Theoretical massNumber of molelcules
Total (without water)26,0732
Polymers26,0732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-21 kcal/mol
Surface area9910 Å2
MethodPISA
3
E: Avidin/streptavidin
F: Avidin/streptavidin


Theoretical massNumber of molelcules
Total (without water)26,0732
Polymers26,0732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-21 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.332, 63.503, 67.745
Angle α, β, γ (deg.)103.83, 107.28, 103.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Avidin/streptavidin


Mass: 13036.376 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans (bacteria) / Strain: OS217 / ATCC BAA-1090 / DSM 15013 / Gene: Sden_0912 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12QS6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 3.0 mg/ml protein in 0.1 M in acetic acid, pH 3.0 mixed with 170 mM Bis-Tris pH 6.0-6.8, 2.0 M Sodium Formate, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2009 / Details: optical hutch
RadiationMonochromator: optical hutch / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.07→61 Å / Num. all: 286503 / Num. obs: 257028 / % possible obs: 92.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→60.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.161 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18536 12987 5.1 %RANDOM
Rwork0.15847 ---
obs0.15982 243993 92.49 %-
all-257028 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.928 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.03 Å20.49 Å2
2---0.45 Å20.69 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.07→60.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 0 851 6143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9117785
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75725.852229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48315872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.737156
X-RAY DIFFRACTIONr_chiral_restr0.10.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024306
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.22640
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23936
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2669
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3751.53681
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02625831
X-RAY DIFFRACTIONr_scbond_it2.4832369
X-RAY DIFFRACTIONr_scangle_it3.1224.51898
X-RAY DIFFRACTIONr_rigid_bond_restr1.45436050
X-RAY DIFFRACTIONr_sphericity_free5.813856
X-RAY DIFFRACTIONr_sphericity_bonded6.08435471
LS refinement shellResolution: 1.07→1.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 928 -
Rwork0.26 15999 -
obs--83.35 %

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