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- PDB-2f01: Epi-biotin complex with core streptavidin -

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Basic information

Entry
Database: PDB / ID: 2f01
TitleEpi-biotin complex with core streptavidin
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / protein/ligand interactions / streptavidin / biotin
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 / EPI-BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous with known structure / Resolution: 0.85 Å
AuthorsLe Trong, I. / Aubert, D.G. / Thomas, N.R. / Stenkamp, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: The high-resolution structure of (+)-epi-biotin bound to streptavidin.
Authors: Le Trong, I. / Aubert, D.G. / Thomas, N.R. / Stenkamp, R.E.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600 HETEROGEN IN THIS STRUCTURE, BOTH EPI-BIOTIN (BTQ) AND BIOTIN (BTN) ARE BOUND TO THE PROTEIN, AND ... HETEROGEN IN THIS STRUCTURE, BOTH EPI-BIOTIN (BTQ) AND BIOTIN (BTN) ARE BOUND TO THE PROTEIN, AND HAVE ALTERNATE CONFORMATION IDS ASSIGNED TO THEM. THE PDB HAS CHANGED ATOM NAMES IN THE BIOTIN MOLECULES FROM THOSE USED IN THE PUBLISHED LITERATURE. THE FOLLOWING TABLE SHOWS THE CONVERSION AUTHOR'S NAME PDB NAME O11 O11 O12 O12 C10 C11 C9 C10 C8 C9 C7 C8 C6 C7 C2 C2 C3 C4 C4 C5 C5 C6 S1 S1 N3P N2 N1P N1 C2P C3 O2P O3

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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)27,8169
Polymers26,5632
Non-polymers1,2547
Water4,918273
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,63218
Polymers53,1254
Non-polymers2,50714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)46.390, 93.811, 104.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-22-

TYR

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Components

#1: Protein Streptavidin


Mass: 13281.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-BTQ / EPI-BIOTIN / 5-[(3AS,4R,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: 38% saturated ammonium sulfate, 0.1 M sodium acetate, pH 4.5, 0.2 M sodium chloride, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.54178
SYNCHROTRONSSRL BL11-120.98
Detector
TypeIDDetector
RIGAKU RAXIS II1IMAGE PLATE
MARRESEARCH2IMAGE PLATE
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2siliconSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
20.981
ReflectionResolution: 0.85→50 Å / Num. all: 189859 / Num. obs: 189859 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 0.85→0.86 Å / % possible all: 83

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: isomorphous with known structure
Starting model: PDB entry 1MK5

1mk5


Resolution: 0.85→10 Å / Num. parameters: 18050 / Num. restraintsaints: 22250 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: Anisotropic atomic displacement parameters for the protein and hetero-atoms; isotropic for water molecules.
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 9485 5.3 %RANDOM
Rwork0.155 ---
all0.1552 180225 --
obs0.1562 180225 90.2 %-
Refine analyzeNum. disordered residues: 20 / Occupancy sum hydrogen: 1561 / Occupancy sum non hydrogen: 2097
Refinement stepCycle: LAST / Resolution: 0.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 82 273 2153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0327
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.125
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0

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