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

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Basic information

Entry
Database: PDB / ID: 7cpz
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 / BIOTIN / Avidin
Function and homology information
Biological speciesStreptomyces sp. H036 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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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Assembly

Deposited unit
A: Mature Streptoavidin-C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4172
Polymers20,1721
Non-polymers2441
Water88349
1
A: Mature Streptoavidin-C1
hetero molecules

A: Mature Streptoavidin-C1
hetero molecules

A: Mature Streptoavidin-C1
hetero molecules

A: Mature Streptoavidin-C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6668
Polymers80,6894
Non-polymers9774
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 area9540 Å2
ΔGint-49 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.997, 57.997, 74.847
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

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Components

#1: Protein Mature Streptoavidin-C1 / 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(DE3) (bacteria) / References: UniProt: A0A0M8UVL7
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.56 Å3/Da / Density % sol: 21.16 %
Crystal growTemperature: 298 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 PILATUS 2M / 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: 2.5→41 Å / Num. obs: 4763 / % possible obs: 99.8 % / Redundancy: 20 % / Rpim(I) all: 0.09 / Rrim(I) all: 0.335 / Net I/σ(I): 7.51
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 229 / Rpim(I) all: 0.258 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BC3

2bc3


Resolution: 2.5→37.42 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2611 221 -
Rwork0.206 --
obs0.2085 4763 99.8 %
Displacement parametersBiso mean: 32.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 16 49 986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052964
X-RAY DIFFRACTIONf_angle_d0.85621314
X-RAY DIFFRACTIONf_chiral_restr0.0559139
X-RAY DIFFRACTIONf_plane_restr0.0034167
X-RAY DIFFRACTIONf_dihedral_angle_d22.7386332

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