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- PDB-4bx7: trans-divalent streptavidin bound to biotin-4-fluorescein -

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Basic information

Entry
Database: PDB / ID: 4bx7
Titletrans-divalent streptavidin bound to biotin-4-fluorescein
Components(STREPTAVIDIN) x 2
KeywordsBIOTIN-BINDING PROTEIN / AVIDIN / 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-4-fluorescein / Streptavidin
Similarity search - Component
Biological speciesSTREPTOMYCES AVIDINII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 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.

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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)28,1404
Polymers27,3772
Non-polymers7632
Water1,40578
1
A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules

A: STREPTAVIDIN
B: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2818
Polymers54,7554
Non-polymers1,5264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area10150 Å2
ΔGint-81.3 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.410, 64.410, 103.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

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Components

#1: Protein STREPTAVIDIN


Mass: 13321.397 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DEAD VARIANT / 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: 14056.019 Da / Num. of mol.: 1
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-B4F / biotin-4-fluorescein


Mass: 644.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H32N4O8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.42 Å3/Da / Density % sol: 48.8 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 65% V/V MPD, 0.1 M MES PH 4.0. CRYSTALS WERE OBTAINED BY THE SITTING-DROP VAPOR-DIFFUSION METHOD AT 277 K, REACHED A MAXIMUM SIZE AFTER 14 DAYS AND WERE HARVESTED SOON AFTER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.26→49.06 Å / Num. obs: 12059 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 42.43 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.95
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 10 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.26 / % possible all: 99.4

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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: 2.26→49.064 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 24.02 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2369 576 4.8 %
Rwork0.1839 --
obs0.1863 12056 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.1 Å2
Refinement stepCycle: LAST / Resolution: 2.26→49.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 54 78 1899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061870
X-RAY DIFFRACTIONf_angle_d0.942566
X-RAY DIFFRACTIONf_dihedral_angle_d14.912623
X-RAY DIFFRACTIONf_chiral_restr0.057280
X-RAY DIFFRACTIONf_plane_restr0.003353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2602-2.48770.24751460.20962808X-RAY DIFFRACTION100
2.4877-2.84760.31411430.21222815X-RAY DIFFRACTION100
2.8476-3.58760.23291380.1852864X-RAY DIFFRACTION100
3.5876-49.07530.21691490.17212993X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0671-0.02480.03570.0199-0.05510.16230.2325-0.06140.0588-0.0516-0.0792-0.0669-0.05650.09090.02930.3432-0.0930.04640.2860.07020.370961.529835.51596.7429
20.174-0.1109-0.07610.11290.08090.13420.1166-0.0825-0.0882-0.0783-0.0063-0.0302-0.3121-0.07680.00690.3066-0.0882-0.01140.2430.02780.281158.783839.15828.9531
30.0059-0.07570.07220.0031-0.10080.5080.0388-0.14480.0886-0.0078-0.0141-0.1018-0.1389-0.2648-0.00750.231-0.0166-0.01620.20330.05550.238652.393437.03556.9779
40.0244-0.0250.0181-0.0309-0.0340.0606-0.02420.2425-0.16170.1401-0.0203-0.0606-0.0327-0.2533-0.00010.19070.06730.00390.3420.04380.223443.035537.90358.2478
50.04810.0199-0.02080.00620.00170.01520.0729-0.02270.2098-0.0755-0.0729-0.1627-0.2231-0.04390.03670.9648-0.01260.14870.09750.11260.446450.937157.631412.5923
60.4878-0.116-0.130.04610.10530.31630.50930.14940.2492-0.0523-0.0514-0.1346-0.4003-0.09020.19330.52870.06880.04910.22930.09740.303749.137250.8454.5545
71.01090.10850.37420.14150.00130.45390.3032-0.1521-0.1750.0782-0.0086-0.0182-0.7218-0.21490.10490.54090.05990.03110.20690.01730.258449.579550.963515.3526
80.8544-0.1760.17450.181-0.10890.06470.4697-0.34980.03220.1156-0.13230.2402-0.28650.1030.15040.35580.01820.03780.1976-0.00230.247348.017944.016921.6333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 15 THROUGH 44 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 45 THROUGH 78 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 79 THROUGH 112 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 113 THROUGH 133 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 16 THROUGH 52 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 53 THROUGH 78 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 79 THROUGH 112 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 113 THROUGH 133 )

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