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- PDB-3wzp: Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/... -

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Basic information

Entry
Database: PDB / ID: 3wzp
TitleCrystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.2 A resolution
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / beta-barrel
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
Chem-ZOF / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Tsumoto, K. / Kodama, T. ...Kawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Tsumoto, K. / Kodama, T. / Kanai, M. / Doi, H. / Inoue, T. / Sugiyama, A.
CitationJournal: J.Biochem. / Year: 2015
Title: Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.
Authors: Kawato, T. / Mizohata, E. / Shimizu, Y. / Meshizuka, T. / Yamamoto, T. / Takasu, N. / Matsuoka, M. / Matsumura, H. / Kodama, T. / Kanai, M. / Doi, H. / Inoue, T. / Sugiyama, A.
History
DepositionOct 1, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,79513
Polymers52,9094
Non-polymers1,8869
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-52 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.969, 57.500, 71.807
Angle α, β, γ (deg.)90.00, 103.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin


Mass: 13227.240 Da / Num. of mol.: 4 / Fragment: UNP residues 37-163 / Mutation: Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pCold TF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: P22629
#2: Chemical
ChemComp-ZOF / 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid


Mass: 356.484 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H28N4O3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium citrate tribasic dehydrate, 0.1 M HEPES sodium, 35%(w/v) (+/-)-2-methyl-2, 4-pentandiol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 148314 / Num. obs: 143314 / % possible obs: 96.6 % / Redundancy: 3.5 % / Rsym value: 0.068 / Net I/σ(I): 18.3
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.75 / Num. unique all: 148314 / Rsym value: 0.309 / % possible all: 96.6

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WYQ

3wyq


Resolution: 1.2→15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.083 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16056 7184 5 %RANDOM
Rwork0.1335 ---
obs0.13487 135778 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.669 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.1 Å2
2---0.15 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 126 441 4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0213881
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2721.9225319
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1525.068146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26215518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.244158
X-RAY DIFFRACTIONr_chiral_restr0.3230.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022940
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.971.52446
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.22423896
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.03931435
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5924.51407
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.74933881
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 534 -
Rwork0.236 9402 -
obs--91.99 %
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)
10.2269-0.063-0.08050.3126-0.08780.13580.00920.0044-0.0221-0.00220.01460.02710.0279-0.0211-0.02390.017-0.004-0.01090.0220.00270.014322.198-8.011620.9219
20.233-0.0062-0.02060.19120.05340.30040.01960.02810.0213-0.01640.02080.0057-0.05490.0033-0.04040.01960.00470.00430.02290.00240.011824.7686.253715.0013
30.3107-0.08040.10270.35020.08350.23330.00960.0210.0191-0.00790.0202-0.0567-0.03070.0345-0.02980.0105-0.00330.00080.0217-0.0030.021551.26460.885720.9063
40.2783-0.00770.0660.3096-0.17240.45180.02960.0353-0.0341-0.03270.0175-0.01640.07480.0186-0.0470.0170.0098-0.00820.0158-0.00850.013848.4703-13.470914.9801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 134
2X-RAY DIFFRACTION1A201 - 203
3X-RAY DIFFRACTION1A301 - 425
4X-RAY DIFFRACTION2B11 - 133
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION2B301 - 401
7X-RAY DIFFRACTION3C12 - 134
8X-RAY DIFFRACTION3C201 - 202
9X-RAY DIFFRACTION3C301 - 410
10X-RAY DIFFRACTION4D11 - 133
11X-RAY DIFFRACTION4D201 - 203
12X-RAY DIFFRACTION4D301 - 405

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