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- PDB-1rxk: crystal structure of streptavidin mutant (M3) a combination of M1+M2 -

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Basic information

Entry
Database: PDB / ID: 1rxk
Titlecrystal structure of streptavidin mutant (M3) a combination of M1+M2
ComponentsStreptavidin
KeywordsUNKNOWN FUNCTION / avidin / streptavidin / pseudo enzymatic activity
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
Chem-BNI / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEisenberg-Domovich, Y. / Pazy, Y. / Nir, O. / Raboy, B. / Bayer, E.A. / Wilchek, M. / Livnah, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural elements responsible for conversion of streptavidin to a pseudoenzyme.
Authors: Eisenberg-Domovich, Y. / Pazy, Y. / Nir, O. / Raboy, B. / Bayer, E.A. / Wilchek, M. / Livnah, O.
History
DepositionDec 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / 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 / _pdbx_database_remark.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999sequence In this streptavidin mutant (M3) the L3,4 loop (sequence: GNAES) was substituted with the ...sequence In this streptavidin mutant (M3) the L3,4 loop (sequence: GNAES) was substituted with the loop from avidin (sequence: TATSNEIK) in addition to the mutaion L124R

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3804
Polymers26,6512
Non-polymers7292
Water2,756153
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7608
Polymers53,3024
Non-polymers1,4584
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12000 Å2
ΔGint-21 kcal/mol
Surface area20050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.335, 81.579, 90.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-574-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, -z+1/2

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Components

#1: Protein Streptavidin


Mass: 13325.478 Da / Num. of mol.: 2 / Mutation: L124R
Source method: isolated from a genetically manipulated source
Details: Streptavidin mutant M3 / Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pET-21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22629
#2: Chemical ChemComp-BNI / 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE / BIOTINYL P-NITROANILINE


Mass: 364.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N4O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 1.5M AS, 0.1M Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.003 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 1.7→56.8 Å / Num. obs: 31858 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→1.73 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→56.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.005 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23905 1607 5.1 %RANDOM
Rwork0.19955 ---
all0.213 ---
obs0.20153 30020 96.2 %-
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 mean: 17.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---1.4 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 50 153 2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211933
X-RAY DIFFRACTIONr_bond_other_d0.0020.021632
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9172641
X-RAY DIFFRACTIONr_angle_other_deg0.86333774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4045241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022180
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02414
X-RAY DIFFRACTIONr_nbd_refined0.1870.2288
X-RAY DIFFRACTIONr_nbd_other0.2590.21852
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21108
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1261.51191
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99621891
X-RAY DIFFRACTIONr_scbond_it2.793742
X-RAY DIFFRACTIONr_scangle_it4.4264.5750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.747 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 112
Rwork0.227 2157

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