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- PDB-3mg5: Core-streptavidin mutant F130L in complex with biotin -

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Basic information

Entry
Database: PDB / ID: 3mg5
TitleCore-streptavidin mutant F130L in complex with biotin
ComponentsStreptavidin
KeywordsBIOTIN-BINDING PROTEIN / Streptavidin
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 / isomorphous to another structure / Resolution: 1.3 Å
AuthorsLe Trong, I. / Baugh, L. / Stayton, P.S. / Lybrand, T.P. / Stenkamp, R.E.
CitationJournal: Biochemistry / Year: 2010
Title: A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?
Authors: Baugh, L. / Le Trong, I. / Cerutti, D.S. / Gulich, S. / Stayton, P.S. / Stenkamp, R.E. / Lybrand, T.P.
History
DepositionApr 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)54,98019
Polymers52,9894
Non-polymers1,99015
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14570 Å2
ΔGint-50 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.910, 97.530, 52.680
Angle α, β, γ (deg.)90.00, 112.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin


Mass: 13247.319 Da / Num. of mol.: 4 / Fragment: CORE STREPTAVIDIN (RESIDUES 13-139) / Mutation: F154L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22629
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 16% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2008 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. all: 121722 / Num. obs: 121722 / % possible obs: 76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.1
Reflection shellResolution: 1.17→1.35 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 0.7 / % possible all: 14.5

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Processing

Software
NameVersionClassification
CCP4model building
REFMAC5.5.0047refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: isomorphous to another structure
Starting model: 1MEP

1mep


Resolution: 1.3→48.74 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.726 / SU ML: 0.032 / σ(F): 0 / σ(I): 0 / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 5484 5 %RANDOM
Rwork0.132 ---
all0.134 104826 --
obs0.134 104826 94.69 %-
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: 13.964 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-1.48 Å2
2---0.42 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.3→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 130 530 4229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213861
X-RAY DIFFRACTIONr_bond_other_d0.0010.022443
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9315266
X-RAY DIFFRACTIONr_angle_other_deg1.04635954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26523.642151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44315524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0031518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02792
X-RAY DIFFRACTIONr_mcbond_it4.18642348
X-RAY DIFFRACTIONr_mcbond_other5.26641011
X-RAY DIFFRACTIONr_mcangle_it5.2363760
X-RAY DIFFRACTIONr_scbond_it5.18461513
X-RAY DIFFRACTIONr_scangle_it6.161506
X-RAY DIFFRACTIONr_rigid_bond_restr3.24736304
X-RAY DIFFRACTIONr_sphericity_free15.8223530
X-RAY DIFFRACTIONr_sphericity_bonded10.10936228
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 280 -
Rwork0.217 5181 -
obs--63.69 %

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