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- PDB-5vl8: Coordination Chemistry within a Protein Host: Regulation of the S... -

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Basic information

Entry
Database: PDB / ID: 5vl8
TitleCoordination Chemistry within a Protein Host: Regulation of the Secondary Coordination Sphere
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / streptavidin / biotin / copper / azide / secondary coordination sphere / hydrogen bond
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
COPPER (II) ION / Chem-S32 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMann, S.I. / Heinisch, T. / Ward, T.R. / Borovik, A.S.
CitationJournal: Chem. Commun. (Camb.) / Year: 2018
Title: Coordination chemistry within a protein host: regulation of the secondary coordination sphere.
Authors: Mann, S.I. / Heinisch, T. / Ward, T.R. / Borovik, A.S.
History
DepositionApr 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3164
Polymers16,5701
Non-polymers7463
Water1,67593
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,26416
Polymers66,2804
Non-polymers2,98412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area11100 Å2
ΔGint-79 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.580, 57.580, 183.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

#1: Protein Streptavidin /


Mass: 16570.018 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
#2: Chemical ChemComp-S32 / [N-(3-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}propyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](hydroxy)copper


Mass: 590.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38CuN6O3S
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 26 mg/mL protein, 2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 1.7→54.9 Å / Num. obs: 17570 / % possible obs: 100 % / Redundancy: 8.7 % / Net I/σ(I): 9.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 904 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1STP

1stp


Resolution: 1.7→54.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.518 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21542 844 4.8 %RANDOM
Rwork0.17565 ---
obs0.17763 16699 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0 Å2
2---0.3 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.7→54.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 45 93 1053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02987
X-RAY DIFFRACTIONr_bond_other_d0.0020.02831
X-RAY DIFFRACTIONr_angle_refined_deg3.431.9711346
X-RAY DIFFRACTIONr_angle_other_deg1.59331897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.9523.65941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43915127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.498155
X-RAY DIFFRACTIONr_chiral_restr0.1240.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021121
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02238
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_it2.2612.243487
X-RAY DIFFRACTIONr_mcbond_other2.2612.239486
X-RAY DIFFRACTIONr_mcangle_it3.4163.347607
X-RAY DIFFRACTIONr_mcangle_other3.4143.352608
X-RAY DIFFRACTIONr_scbond_it3.112.529499
X-RAY DIFFRACTIONr_scbond_other3.062.53499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6543.659737
X-RAY DIFFRACTIONr_long_range_B_refined6.81519.4481130
X-RAY DIFFRACTIONr_long_range_B_other6.78819.4471130
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 53 -
Rwork0.362 1204 -
obs--100 %

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