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- PDB-3re5: Crystal structure of R4-6 streptavidin -

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Basic information

Entry
Database: PDB / ID: 3re5
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: 1.949 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)16,3273
Polymers15,9961
Non-polymers3302
Water1,44180
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)65,30712
Polymers63,9864
Non-polymers1,3218
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 area11740 Å2
ΔGint-62 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.471, 57.471, 173.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-174-

HOH

21A-176-

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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 45.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 MgCl2, 0.1 HEPES, pH 7.5, 25% PEG 3350, 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: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.949→20 Å / Num. obs: 11127 / % possible obs: 99.9 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.5
Reflection shellResolution: 1.949→1.98 Å / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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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: 1.949→19.78 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2166 / WRfactor Rwork: 0.1861 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8291 / SU B: 7.761 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1599 / SU Rfree: 0.1457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 529 4.8 %RANDOM
Rwork0.2039 ---
obs0.2052 11079 99.91 %-
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: 61.26 Å2 / Biso mean: 30.733 Å2 / Biso min: 10.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.949→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 22 80 1017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211017
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9171387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8085135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.824.61539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72315135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.044153
X-RAY DIFFRACTIONr_chiral_restr0.1110.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02768
X-RAY DIFFRACTIONr_mcbond_it1.153.5653
X-RAY DIFFRACTIONr_mcangle_it3.843501038
X-RAY DIFFRACTIONr_scbond_it7.76350364
X-RAY DIFFRACTIONr_scangle_it0.934.5348
LS refinement shellResolution: 1.949→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 33 -
Rwork0.238 769 -
all-802 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: -13.6695 Å / Origin y: -24.7021 Å / Origin z: -2.3005 Å
111213212223313233
T0.0421 Å20.0094 Å20.0029 Å2-0.0493 Å2-0.0139 Å2--0.0168 Å2
L1.6353 °2-0.1744 °20.3128 °2-0.9066 °2-0.1428 °2--0.8571 °2
S0.0206 Å °0.0231 Å °-0.086 Å °-0.0491 Å °0.0562 Å °-0.0622 Å °0.0164 Å °0.1256 Å °-0.0768 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 135
2X-RAY DIFFRACTION1A300
3X-RAY DIFFRACTION1A700

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