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- PDB-2gh7: Epi-biotin complex with core streptavidin -

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Basic information

Entry
Database: PDB / ID: 2gh7
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / EPI-BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1 Å
AuthorsLe Trong, I. / Aubert, D.G.L. / 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
DepositionMar 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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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) / Production host: Escherichia coli (E. coli) / 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

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 42.49 %
Crystal growMethod: vapor diffusion / pH: 7
Details: Protein solution - 10 mg/mL, 10mM Tris Hl, pH 7.0 Reservoir - 38% saturate ammonium sulfate, 0.1 M sodium acetate, pH 4.5,0.2 M NaCl , VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979454 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979454 Å / Relative weight: 1
ReflectionResolution: 0.85→30 Å / Num. all: 189859 / Num. obs: 189859 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 55.5
Reflection shellResolution: 0.85→0.86 Å / % possible all: 83

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1→10 Å / Num. parameters: 18050 / Num. restraintsaints: 22250 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1523 5936 5 %RANDOM
all0.1439 118725 --
obs0.141 -92 %-
Refine analyzeNum. disordered residues: 20 / Occupancy sum hydrogen: 1561 / Occupancy sum non hydrogen: 2097
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 82 273 2153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0325
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.113
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0

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