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- PDB-3rdu: Crystal structure of R7-2 streptavidin complexed with PEG -

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Basic information

Entry
Database: PDB / ID: 3rdu
TitleCrystal structure of R7-2 streptavidin complexed with PEG
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / Streptavidin variants / improved desthiobiotin binding / opened loop destabilization
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Magalhaes, M. / Czecster, C.M. / Guan, R. / Levy, M. / Almo, S.C.
CitationJournal: Protein Sci. / Year: 2011
Title: Evolved streptavidin mutants reveal key role of loop residue in high-affinity binding.
Authors: Magalhaes, M.L. / Czekster, C.M. / Guan, R. / Malashkevich, V.N. / Almo, S.C. / Levy, M.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4815
Polymers15,9661
Non-polymers5154
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,92420
Polymers63,8664
Non-polymers2,05816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area15110 Å2
ΔGint-73 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.354, 57.354, 76.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-177-

HOH

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Components

#1: Protein Streptavidin /


Mass: 15966.381 Da / Num. of mol.: 1 / Fragment: UNP Residues 37-164 / Mutation: T90S,W108V,L110T,F29L,S52G,R53S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pCR2.1-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: P22629
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.98 Å3/Da / Density % sol: 37.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG1000, 10% PEG8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 21154 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Χ2: 2.23 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.537.20.57310231.518199.9
1.53-1.557.40.49910331.51199.8
1.55-1.587.50.47210271.482199.9
1.58-1.627.40.41210381.585199.8
1.62-1.657.30.33510461.63199.9
1.65-1.697.20.29710371.6451100
1.69-1.737.10.25510311.717199.9
1.73-1.7870.2110621.7971100
1.78-1.836.80.17510431.884199.9
1.83-1.896.60.14710412.042199.8
1.89-1.966.30.11710342.201199.4
1.96-2.046.30.10310502.271199.7
2.04-2.1360.0910652.509199.7
2.13-2.246.10.0810482.624199.5
2.24-2.386.10.07610662.668199.8
2.38-2.566.30.07110592.709199.7
2.56-2.826.50.06510763.039199.6
2.82-3.236.70.0610803.361199.5
3.23-4.077.20.05511073.568199.8
4.07-507.10.04911883.028198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.5 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.92 Å
Translation2.5 Å31.92 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RDM

3rdm


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2093 / WRfactor Rwork: 0.1722 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8711 / SU B: 2.498 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0833 / SU Rfree: 0.0732 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 1089 5.2 %RANDOM
Rwork0.1696 ---
obs0.1714 21100 99.67 %-
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 max: 105.32 Å2 / Biso mean: 16.5569 Å2 / Biso min: 8.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å2-0 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 34 117 1056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021973
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9261326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.48324.59537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.29115127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.689153
X-RAY DIFFRACTIONr_chiral_restr0.0860.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02728
X-RAY DIFFRACTIONr_mcbond_it1.2863.5616
X-RAY DIFFRACTIONr_mcangle_it2.70550982
X-RAY DIFFRACTIONr_scbond_it4.02350357
X-RAY DIFFRACTIONr_scangle_it1.6284.5342
X-RAY DIFFRACTIONr_rigid_bond_restr0.8663973
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 98 -
Rwork0.233 1404 -
all-1502 -
obs--99.34 %
Refinement TLS params.Method: refined / Origin x: 14.6253 Å / Origin y: 3.9798 Å / Origin z: -3.0741 Å
111213212223313233
T0.0072 Å20.004 Å20.006 Å2-0.0137 Å2-0.0102 Å2--0.021 Å2
L0.8495 °2-0.0058 °2-0.0528 °2-0.8121 °20.054 °2--0.5169 °2
S0.0131 Å °0.0259 Å °-0.0077 Å °-0.0582 Å °0.0301 Å °-0.1222 Å °0.0331 Å °0.0781 Å °-0.0432 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 135
2X-RAY DIFFRACTION1A500 - 503
3X-RAY DIFFRACTION1A700

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