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- PDB-4ggz: The structure of bradavidin2-biotin complex -

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Basic information

Entry
Database: PDB / ID: 4ggz
TitleThe structure of bradavidin2-biotin complex
ComponentsBradavidin 2
KeywordsBIOTIN BINDING PROTEIN / bradavidin / avidin / oligomeric state / streptavidin / high affinity systems / lipocalin fold / beta barrel
Function / homology
Function and homology information


biotin binding / 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
BIOTIN / Bll1558 protein
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLivnah, O. / Meir, A.
CitationJournal: Protein Sci. / Year: 2013
Title: The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins.
Authors: Leppiniemi, J. / Meir, A. / Kahkonen, N. / Kukkurainen, S. / Maatta, J.A. / Ojanen, M. / Janis, J. / Kulomaa, M.S. / Livnah, O. / Hytonen, V.P.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.3Nov 27, 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: Bradavidin 2
B: Bradavidin 2
C: Bradavidin 2
D: Bradavidin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3028
Polymers50,3254
Non-polymers9774
Water7,278404
1
A: Bradavidin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8252
Polymers12,5811
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bradavidin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8252
Polymers12,5811
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bradavidin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8252
Polymers12,5811
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bradavidin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8252
Polymers12,5811
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.067, 95.434, 49.947
Angle α, β, γ (deg.)90.00, 113.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Bradavidin 2 / Bll1558 protein


Mass: 12581.157 Da / Num. of mol.: 4 / Fragment: UNP residues 19-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bll1558 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q89U61
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 283 K / Method: liquid diffusion / pH: 9
Details: 10% PEG20000, 2% 1,4-dioxane, 0.1 M bicine, pH 9.0, LIQUID DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.75→71.839 Å / Num. all: 51302 / Num. obs: 51302 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GGR

4ggr


Resolution: 1.75→71.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.778 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24026 2599 5.1 %RANDOM
Rwork0.19244 ---
obs0.19483 48501 99.32 %-
all-48501 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.26 Å2
2---0.34 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→71.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 64 404 3772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223671
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9395075
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8995490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11523.151146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92715533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9861516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022864
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21547
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22467
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2357
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9951.52262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63123621
X-RAY DIFFRACTIONr_scbond_it2.53331676
X-RAY DIFFRACTIONr_scangle_it3.4844.51421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 194 -
Rwork0.266 3498 -
obs--97.54 %

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