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- PDB-5to2: Crystal structure of streptavidin with one wild type subunit and ... -

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Basic information

Entry
Database: PDB / ID: 5to2
TitleCrystal structure of streptavidin with one wild type subunit and three mutated subunits (N23A/S27D/S45A)
Components(Streptavidin) x 2
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
DI(HYDROXYETHYL)ETHER / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZhang, M. / Biswas, S. / Deng, W. / Yu, H.
CitationJournal: To Be Published
Title: Crystal structure of streptavidin with one wild type subunit and three mutated subunits (N23A/S27D/S45A)
Authors: Zhang, M. / Biswas, S. / Deng, W. / Yu, H.
History
DepositionOct 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)52,2515
Polymers52,1444
Non-polymers1061
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-54 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.357, 56.738, 57.435
Angle α, β, γ (deg.)87.54, 85.89, 67.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Streptavidin


Mass: 13050.129 Da / Num. of mol.: 3 / Mutation: N23A, S27D, S45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein Streptavidin


Mass: 12994.066 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) / References: UniProt: P22629
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.3, 0.25 M MgCl2, 32% PEG4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 62294 / % possible obs: 94.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.8
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.5 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.746 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23365 2988 5.1 %RANDOM
Rwork0.20428 ---
obs0.20575 56087 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.51 Å2-1.18 Å2
2--0.72 Å21.07 Å2
3----0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 7 282 3869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023723
X-RAY DIFFRACTIONr_bond_other_d00.023303
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.8925111
X-RAY DIFFRACTIONr_angle_other_deg3.88337548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.52923.642151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56615494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.721516
X-RAY DIFFRACTIONr_chiral_restr0.0980.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024394
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02934
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2832.4341943
X-RAY DIFFRACTIONr_mcbond_other1.2812.4331942
X-RAY DIFFRACTIONr_mcangle_it2.3023.6422427
X-RAY DIFFRACTIONr_mcangle_other2.3023.6432428
X-RAY DIFFRACTIONr_scbond_it1.3862.4951780
X-RAY DIFFRACTIONr_scbond_other1.3862.4951780
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3323.6752678
X-RAY DIFFRACTIONr_long_range_B_refined4.16927.6624075
X-RAY DIFFRACTIONr_long_range_B_other4.13927.4784051
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 221 -
Rwork0.298 4058 -
obs--93.47 %
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)
10.0392-0.12470.12160.5199-0.37961.2202-0.0219-0.01070.0118-0.1327-0.0519-0.1006-0.1938-0.39850.07380.18730.13510.03220.190.00380.0507-8.441212.45064.4993
20.1228-0.11270.33760.4815-0.23920.9895-0.0511-0.0270.01830.00360.0135-0.1252-0.043-0.0520.03760.120.03320.03090.05390.01010.04252.34975.036514.8258
30.3438-0.25860.2350.2028-0.09711.09-0.00910.00960.0223-0.0069-0.0021-0.0179-0.04610.04050.01120.0703-0.00580.01930.04860.00480.05663.3987-2.956-15.4099
40.0952-0.12650.2980.2496-0.33211.02140.0008-0.0228-0.00610.05430.02430.0310.1448-0.0379-0.02510.11220.03120.02440.03520.01430.0742.842-14.9073-4.0104
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 135
2X-RAY DIFFRACTION2B15 - 135
3X-RAY DIFFRACTION3C15 - 135
4X-RAY DIFFRACTION4D16 - 134

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