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- PDB-7cq0: Crystal structure of Streptoavidin-C1 from Streptomyces cinamonensis -

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Basic information

Entry
Database: PDB / ID: 7cq0
TitleCrystal structure of Streptoavidin-C1 from Streptomyces cinamonensis
ComponentsMature Streptoavidin-C1
KeywordsANTIMICROBIAL PROTEIN / Avidin / Antifungal / Biotin
Function / homologyAvidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / biotin binding / extracellular region / Avidin
Function and homology information
Biological speciesStreptomyces sp. H036 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsJeon, B.J. / Kim, S. / Lee, J.-H. / Kim, M.S. / Hwang, K.Y.
CitationJournal: Iucrj / Year: 2021
Title: Insights into the structure of mature streptavidin C1 from Streptomyces cinnamonensis reveal the self-binding of the extension C-terminal peptide to biotin-binding sites.
Authors: Jeon, B.J. / Kim, S. / Kim, M.S. / Lee, J.H. / Kim, B.S. / Hwang, K.Y.
History
DepositionAug 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Nov 29, 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

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Assembly

Deposited unit
A: Mature Streptoavidin-C1


Theoretical massNumber of molelcules
Total (without water)20,1721
Polymers20,1721
Non-polymers00
Water1,74797
1
A: Mature Streptoavidin-C1

A: Mature Streptoavidin-C1

A: Mature Streptoavidin-C1

A: Mature Streptoavidin-C1


Theoretical massNumber of molelcules
Total (without water)80,6894
Polymers80,6894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area11090 Å2
ΔGint-56 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.442, 58.442, 78.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

21A-278-

HOH

31A-280-

HOH

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Components

#1: Protein Mature Streptoavidin-C1


Mass: 20172.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. H036 (bacteria) / Gene: ADK98_07690
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0M8UVL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.66 Å3/Da / Density % sol: 25.96 %
Crystal growTemperature: 298.15 K / Method: batch mode / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.03→46.88 Å / Num. obs: 16769 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 24.97 Å2 / Rrim(I) all: 0.315 / Net I/σ(I): 6.3
Reflection shellResolution: 2.03→2.09 Å / Num. unique obs: 16769 / Rrim(I) all: 0.315

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hds

6hds


Resolution: 2.03→46.88 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2256 1691 10.08 %
Rwork0.203 15078 -
obs0.2054 16769 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.64 Å2
Refinement stepCycle: LAST / Resolution: 2.03→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 0 97 1156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381087
X-RAY DIFFRACTIONf_angle_d0.62141483
X-RAY DIFFRACTIONf_chiral_restr0.0496159
X-RAY DIFFRACTIONf_plane_restr0.0038192
X-RAY DIFFRACTIONf_dihedral_angle_d25.7251154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.090.26441410.29621254X-RAY DIFFRACTION99.01
2.09-2.160.30111420.28841234X-RAY DIFFRACTION99.57
2.16-2.230.31781430.25671290X-RAY DIFFRACTION100
2.23-2.320.30371390.24371236X-RAY DIFFRACTION99.78
2.32-2.430.27971420.24111272X-RAY DIFFRACTION100
2.43-2.560.2611360.23521238X-RAY DIFFRACTION99.85
2.56-2.720.28711430.2221267X-RAY DIFFRACTION99.86
2.72-2.930.22051390.20261264X-RAY DIFFRACTION100
2.93-3.220.22151360.19051249X-RAY DIFFRACTION99.93
3.22-3.690.1871420.17761253X-RAY DIFFRACTION99.86
3.69-4.640.18191380.151266X-RAY DIFFRACTION99.93
4.65-46.880.18741500.1811255X-RAY DIFFRACTION99.79

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