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- PDB-1swu: STREPTAVIDIN MUTANT Y43F -

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Basic information

Entry
Database: PDB / ID: 1swu
TitleSTREPTAVIDIN MUTANT Y43F
ComponentsSTREPTAVIDIN
KeywordsPROTEIN BINDING / BIOTIN BINDING PROTEIN
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 / Resolution: 1.14 Å
AuthorsFreitag, S. / Le Trong, I. / Klumb, L.A. / Stayton, P.S. / Stenkamp, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Atomic resolution structure of biotin-free Tyr43Phe streptavidin: what is in the binding site?
Authors: Freitag, S. / Le Trong, I. / Klumb, L.A. / Stayton, P.S. / Stenkamp, R.E.
History
DepositionOct 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
C: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,77010
Polymers53,0614
Non-polymers7096
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-119 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.200, 84.900, 46.400
Angle α, β, γ (deg.)90.00, 98.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
STREPTAVIDIN


Mass: 13265.336 Da / Num. of mol.: 4 / Mutation: Y43F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: PET-210 , NOVAGEN, INC., MADISON,WI / Cell line (production host): T7 EXPRESSION SYSTEM / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.93 Å3/Da / Density % sol: 36 %
Crystal growpH: 4.5 / Details: pH 4.5
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein1drop
250 %1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1998
RadiationProtocol: MONOCHROMATIC / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.14→50 Å / Num. obs: 149978 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.6
Reflection shellResolution: 1.14→1.2 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.8 / % possible all: 81
Reflection
*PLUS
Num. measured all: 627749
Reflection shell
*PLUS
Lowest resolution: 1.2 Å / % possible obs: 81 % / Rmerge(I) obs: 0.144

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SWA

1swa


Resolution: 1.14→10 Å / Num. parameters: 38361 / Num. restraintsaints: 48997 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (I>2SIGMA(I)) BY 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.157 14997 10 %EVERY 10TH REFLECTION
all0.126 149978 --
obs0.125 -92.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-218
Refine analyzeNum. disordered residues: 41 / Occupancy sum hydrogen: 3331.3 / Occupancy sum non hydrogen: 3980.1
Refinement stepCycle: LAST / Resolution: 1.14→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 0 598 4262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.002
X-RAY DIFFRACTIONs_zero_chiral_vol0.13
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.159
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.087
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.095
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.125
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.002
X-RAY DIFFRACTIONs_chiral_restr0.13

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