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- PDB-3rdx: Crystal structure of ligand-free R7-2 streptavidin -

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Basic information

Entry
Database: PDB / ID: 3rdx
TitleCrystal structure of ligand-free R7-2 streptavidin
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 ...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: 2.101 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 2, 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

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0253
Polymers31,9332
Non-polymers921
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-12 kcal/mol
Surface area13300 Å2
MethodPISA
2
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0506
Polymers63,8664
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9220 Å2
ΔGint-62 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.250, 81.640, 84.537
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-152-

HOH

21B-166-

HOH

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Components

#1: Protein Streptavidin


Mass: 15966.381 Da / Num. of mol.: 2 / 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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Na acetate, pH 4.5, 3 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 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: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16282 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.099 / Χ2: 1.298 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.145.60.8187951.219199.6
2.14-2.1860.7528041.103199.8
2.18-2.226.30.6598001.241100
2.22-2.266.40.5978161.3181100
2.26-2.316.40.6027891.243199.9
2.31-2.376.40.5058031.292199.9
2.37-2.426.50.4347871.322199.9
2.42-2.496.40.4048191.2211100
2.49-2.566.40.3288111.2651100
2.56-2.656.40.2577871.1881100
2.65-2.746.40.2078211.2241100
2.74-2.856.30.1528121.3121100
2.85-2.986.30.1268051.3081100
2.98-3.146.30.0958191.3521100
3.14-3.336.40.0798141.369199.8
3.33-3.596.30.0648141.3391100
3.59-3.956.30.0568221.5251100
3.95-4.526.30.0518241.564199.9
4.52-5.76.10.0398501.276199.8
5.7-506.20.0378901.254199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3rdu


Resolution: 2.101→19.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2447 / WRfactor Rwork: 0.1854 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7188 / SU B: 11.829 / SU ML: 0.14 / SU R Cruickshank DPI: 0.1644 / SU Rfree: 0.2139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 817 5 %RANDOM
Rwork0.2125 ---
obs0.2156 16197 99.36 %-
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: 96.3 Å2 / Biso mean: 22.1929 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2---0.02 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.101→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 6 109 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211926
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.92644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1895263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.24224.60576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00515263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.594156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021478
X-RAY DIFFRACTIONr_mcbond_it1.2773.51252
X-RAY DIFFRACTIONr_mcangle_it4.006501993
X-RAY DIFFRACTIONr_scbond_it7.55850674
X-RAY DIFFRACTIONr_scangle_it1.3254.5646
X-RAY DIFFRACTIONr_rigid_bond_restr1.3631926
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 62 -
Rwork0.274 1047 -
all-1109 -
obs--95.27 %
Refinement TLS params.

T13: 0.0019 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4431-1.0476-0.4523.10180.98350.86740.05350.0950.113-0.15780.0075-0.0078-0.1058-0.0401-0.0610.0364-0.01610.04160.01490.011922.54197.8031-2.2707
21.8727-0.73210.75612.1013-0.91871.5616-0.01130.1328-0.1822-0.14990.1170.08150.10850.0244-0.10570.0336-0.00390.0494-0.01070.019248.9827-7.8264-2.3703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 134
2X-RAY DIFFRACTION1A141 - 196
3X-RAY DIFFRACTION2B11 - 135
4X-RAY DIFFRACTION2B141 - 193
5X-RAY DIFFRACTION2B300

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