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- PDB-4bx5: cis-divalent streptavidin -

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Basic information

Entry
Database: PDB / ID: 4bx5
Titlecis-divalent streptavidin
Components(STREPTAVIDIN) x 2
KeywordsBIOTIN-BINDING PROTEIN / BIOTIN / AVIDIN
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
Biological speciesSTREPTOMYCES AVIDINII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.431 Å
AuthorsFairhead, M. / Krndija, D. / Lowe, E.D. / Howarth, M.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Plug-and-Play Pairing Via Defined Divalent Streptavidins.
Authors: Fairhead, M. / Krndija, D. / Lowe, E.D. / Howarth, M.
History
DepositionJul 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)55,88610
Polymers55,2494
Non-polymers6376
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-29 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.220, 84.240, 58.250
Angle α, β, γ (deg.)90.00, 98.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein STREPTAVIDIN


Mass: 14343.168 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-163 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P22629
#2: Protein STREPTAVIDIN


Mass: 13281.336 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P22629
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.12 Å3/Da / Density % sol: 41.44 % / Description: NONE
Crystal growpH: 6.5
Details: 2.5 % W/V POLYETHYLENE GLYCOL (PEG) 1000, 12.5 % W/V PEG 3350, 12.5 % V/V MPD, 30 MM OF ETHYLENE GLYCOL MIX (DI-ETHYLENEGLYCOL, TRI-ETHYLENEGLYCOL, TETRA-ETHYLENEGLYCOL, PENTA-ETHYLENEGLYCOL) ...Details: 2.5 % W/V POLYETHYLENE GLYCOL (PEG) 1000, 12.5 % W/V PEG 3350, 12.5 % V/V MPD, 30 MM OF ETHYLENE GLYCOL MIX (DI-ETHYLENEGLYCOL, TRI-ETHYLENEGLYCOL, TETRA-ETHYLENEGLYCOL, PENTA-ETHYLENEGLYCOL) AND 0.1 M MES/IMIDAZOLE PH 6.5, CORRESPONDING TO CONDITION E4 OF THE MORPHEUS SCREEN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: MARRESEARCH 300MM / Detector: CCD / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.43→42.12 Å / Num. obs: 75108 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 14.65 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.21 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RY1

3ry1


Resolution: 1.431→42.12 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1873 3785 5 %
Rwork0.1601 --
obs0.1614 75104 92.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 1.431→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 42 517 4144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013886
X-RAY DIFFRACTIONf_angle_d1.2985335
X-RAY DIFFRACTIONf_dihedral_angle_d11.8581277
X-RAY DIFFRACTIONf_chiral_restr0.081593
X-RAY DIFFRACTIONf_plane_restr0.006679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4309-1.4490.29371380.28132643X-RAY DIFFRACTION92
1.449-1.46810.2711340.26332592X-RAY DIFFRACTION93
1.4681-1.48820.261400.25412570X-RAY DIFFRACTION90
1.4882-1.50950.24811100.23662548X-RAY DIFFRACTION90
1.5095-1.5320.25141330.2242307X-RAY DIFFRACTION80
1.532-1.55590.23231270.21272489X-RAY DIFFRACTION89
1.5559-1.58150.2571270.21262715X-RAY DIFFRACTION94
1.5815-1.60870.25381600.20472666X-RAY DIFFRACTION95
1.6087-1.6380.25931460.19492701X-RAY DIFFRACTION95
1.638-1.66950.21431330.18862743X-RAY DIFFRACTION95
1.6695-1.70360.23911490.19062676X-RAY DIFFRACTION95
1.7036-1.74060.21771650.17872689X-RAY DIFFRACTION95
1.7406-1.78110.21671400.17782745X-RAY DIFFRACTION95
1.7811-1.82560.21011450.1752659X-RAY DIFFRACTION95
1.8256-1.8750.20341570.16812692X-RAY DIFFRACTION94
1.875-1.93020.20321180.16162681X-RAY DIFFRACTION94
1.9302-1.99250.19371450.16352641X-RAY DIFFRACTION93
1.9925-2.06370.18681370.16332569X-RAY DIFFRACTION91
2.0637-2.14630.18991210.15892331X-RAY DIFFRACTION81
2.1463-2.2440.21291380.15442671X-RAY DIFFRACTION94
2.244-2.36230.18211560.15472745X-RAY DIFFRACTION96
2.3623-2.51030.19691610.15142718X-RAY DIFFRACTION96
2.5103-2.70410.17431450.14932766X-RAY DIFFRACTION96
2.7041-2.97610.16691580.14082688X-RAY DIFFRACTION95
2.9761-3.40660.14491410.13622720X-RAY DIFFRACTION94
3.4066-4.29130.14471200.12472476X-RAY DIFFRACTION86
4.2913-42.13820.16081410.15052878X-RAY DIFFRACTION98

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