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- PDB-3rdm: Crystal structure of R7-2 streptavidin complexed with biotin/PEG -

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Basic information

Entry
Database: PDB / ID: 3rdm
TitleCrystal structure of R7-2 streptavidin complexed with biotin/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 ...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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4493
Polymers15,9661
Non-polymers4832
Water2,288127
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)65,79612
Polymers63,8664
Non-polymers1,9308
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 area13920 Å2
ΔGint-53 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.436, 57.436, 173.958
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-183-

HOH

21A-232-

HOH

31A-248-

HOH

41A-264-

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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 MgCl2, 0.1 Bis-Tris, pH 5.5, 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: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 19742 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.077 / Χ2: 2.201 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.666.10.36719191.032199.5
1.66-1.726.50.30519371.1141100
1.72-1.86.50.22519421.317199.9
1.8-1.96.50.17619401.586199.9
1.9-2.026.40.13319401.8941100
2.02-2.176.40.10919662.318199.9
2.17-2.396.50.09719812.5761100
2.39-2.746.60.08619982.9781100
2.74-3.456.30.07220053.7611100
3.45-505.90.05521143.326198

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.21 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.72 Å
Translation2.5 Å28.72 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IZI

2izi


Resolution: 1.6→19.17 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2373 / WRfactor Rwork: 0.2091 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8603 / SU B: 3.221 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0958 / SU Rfree: 0.0955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 1012 5.1 %RANDOM
Rwork0.2151 ---
obs0.2165 19708 99.79 %-
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: 50.81 Å2 / Biso mean: 21.471 Å2 / Biso min: 4.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 32 127 1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021969
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9271325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7545128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.48724.59537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60215128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.029153
X-RAY DIFFRACTIONr_chiral_restr0.1040.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02728
X-RAY DIFFRACTIONr_mcbond_it1.0613.5610
X-RAY DIFFRACTIONr_mcangle_it2.91350972
X-RAY DIFFRACTIONr_scbond_it5.55250359
X-RAY DIFFRACTIONr_scangle_it1.0674.5351
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 67 -
Rwork0.234 1332 -
all-1399 -
obs--99.01 %
Refinement TLS params.Method: refined / Origin x: -13.8528 Å / Origin y: -24.4766 Å / Origin z: -2.4905 Å
111213212223313233
T0.082 Å20.0159 Å20.0001 Å2-0.0907 Å2-0.0135 Å2--0.035 Å2
L1.2158 °20.0072 °20.0742 °2-0.7932 °2-0.0401 °2--0.37 °2
S0.0097 Å °0.024 Å °-0.0747 Å °-0.0705 Å °0.068 Å °-0.0862 Å °0.0154 Å °0.0889 Å °-0.0777 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 147
2X-RAY DIFFRACTION1A700

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