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- PDB-6rtq: Hoefavidin P61C mutant generates a stabilized octamer -

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Basic information

Entry
Database: PDB / ID: 6rtq
TitleHoefavidin P61C mutant generates a stabilized octamer
ComponentsHoefavidin
KeywordsBIOTIN BINDING PROTEIN / AVIDIN / BIOTIN / PROTEIN ASSEMBLY / HIGH AFFINITY SYSTEMS / DIMERIC AVIDINS
Function / homology
Function and homology information


biotin binding / protein homodimerization activity / extracellular region
Similarity search - Function
Avidin-like / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHoeflea phototrophica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLivnah, O. / Avraham, O.
CitationJournal: Crystals / Year: 2019
Title: Generating a High Valency Biotin Binder by Selecting Uniform Protein Assemblies via Crystallization
Authors: Avraham, O. / Levi-Kalisman, Y. / Livnah, O.
History
DepositionMay 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hoefavidin
B: Hoefavidin


Theoretical massNumber of molelcules
Total (without water)31,1622
Polymers31,1622
Non-polymers00
Water1,38777
1
A: Hoefavidin
B: Hoefavidin

A: Hoefavidin
B: Hoefavidin

A: Hoefavidin
B: Hoefavidin

A: Hoefavidin
B: Hoefavidin


Theoretical massNumber of molelcules
Total (without water)124,6478
Polymers124,6478
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area26290 Å2
ΔGint-171 kcal/mol
Surface area39650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.885, 81.885, 130.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

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Components

#1: Protein Hoefavidin


Mass: 15580.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hoeflea phototrophica (strain DSM 17068 / NCIMB 14078 / DFL-43) (bacteria)
Strain: DSM 17068 / NCIMB 14078 / DFL-43 / Gene: HPDFL43_17171 / Variant: DSM 17068 / NCIMB 14078 / DFL-43 / Production host: Escherichia coli (E. coli) / References: UniProt: A9D857
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5-1.8 M LI2SO4 AND 0.1 M HEPES (PH 7.5-7.7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2017 / Details: optical hutch
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→43.48 Å / Num. obs: 18089 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.784 / Num. unique obs: 1313 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z6J

4z6j


Resolution: 2→40.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.771 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.201 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 891 4.9 %RANDOM
Rwork0.227 ---
obs0.23 17153 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0.58 Å20 Å2
2---1.16 Å20 Å2
3---3.75 Å2
Refinement stepCycle: LAST / Resolution: 2→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 77 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122050
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181682
X-RAY DIFFRACTIONr_angle_refined_deg2.081.6292802
X-RAY DIFFRACTIONr_angle_other_deg1.4631.5593938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3955264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37726.08792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02815280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022372
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02428
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_it7.6695.9711062
X-RAY DIFFRACTIONr_mcbond_other7.6675.9681061
X-RAY DIFFRACTIONr_mcangle_it9.3958.9311324
X-RAY DIFFRACTIONr_mcangle_other9.3938.9341325
X-RAY DIFFRACTIONr_scbond_it7.9366.368985
X-RAY DIFFRACTIONr_scbond_other7.9356.36983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.519.3551476
X-RAY DIFFRACTIONr_long_range_B_refined12.62469.8892283
X-RAY DIFFRACTIONr_long_range_B_other12.62769.8652278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 55 -
Rwork0.394 1253 -
obs--100 %

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