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- PDB-3re6: Crystal structure of R4-6 streptavidin -

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Basic information

Entry
Database: PDB / ID: 3re6
TitleCrystal structure of R4-6 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: 1.823 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0892
Polymers15,9961
Non-polymers921
Water1,74797
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)64,3548
Polymers63,9864
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445-y-1,-x-1,-z1
crystal symmetry operation10_445-x-1,-y-1,z1
crystal symmetry operation15_555y,x,-z1
Buried area9460 Å2
ΔGint-53 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.476, 57.476, 173.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-160-

HOH

21A-170-

HOH

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Components

#1: Protein Streptavidin


Mass: 15996.406 Da / Num. of mol.: 1 / Fragment: UNP Residues 37-164 / Mutation: T90S,W108V,L110T,F29L,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.: 97 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 8000, 0.1 M Na-cacodylate, pH 6.5, 0.2 M Ca-acetate, 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: 1.82→20 Å / Num. obs: 13522 / % possible obs: 99.6 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.093
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 13 % / Rmerge(I) obs: 0.539 / Num. unique all: 617 / Rsym value: 0.539 / % possible all: 92

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3rds


Resolution: 1.823→19.79 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.1812 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8721 / SU B: 4.415 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1194 / SU Rfree: 0.1214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 666 4.9 %RANDOM
Rwork0.1902 ---
obs0.1921 13481 99.99 %-
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: 65.17 Å2 / Biso mean: 25.94 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.823→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms891 0 6 97 994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021932
X-RAY DIFFRACTIONr_angle_refined_deg1.171.9091277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.63824.32437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29415127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.229153
X-RAY DIFFRACTIONr_chiral_restr0.0790.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02708
X-RAY DIFFRACTIONr_mcbond_it1.0053.5596
X-RAY DIFFRACTIONr_mcangle_it3.1850949
X-RAY DIFFRACTIONr_scbond_it6.25650336
X-RAY DIFFRACTIONr_scangle_it0.8514.5326
LS refinement shellResolution: 1.823→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 60 -
Rwork0.201 911 -
all-971 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -13.4696 Å / Origin y: -24.5671 Å / Origin z: -2.1331 Å
111213212223313233
T0.0209 Å20.004 Å20.0031 Å2-0.0452 Å2-0.022 Å2--0.0211 Å2
L1.3591 °2-0.087 °20.0714 °2-0.8966 °2-0.0222 °2--0.8684 °2
S0.0246 Å °0.0178 Å °-0.0874 Å °-0.0619 Å °0.0642 Å °-0.0685 Å °0.0014 Å °0.1694 Å °-0.0887 Å °

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