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- PDB-4ggt: Structure of apo Bradavidin2 (Form B) -

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Basic information

Entry
Database: PDB / ID: 4ggt
TitleStructure of apo Bradavidin2 (Form B)
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
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.693 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bradavidin 2
B: Bradavidin 2


Theoretical massNumber of molelcules
Total (without water)25,1622
Polymers25,1622
Non-polymers00
Water2,432135
1
A: Bradavidin 2


Theoretical massNumber of molelcules
Total (without water)12,5811
Polymers12,5811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bradavidin 2


Theoretical massNumber of molelcules
Total (without water)12,5811
Polymers12,5811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.771, 46.118, 46.449
Angle α, β, γ (deg.)106.59, 106.92, 106.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bradavidin 2 / Bll1558 protein


Mass: 12581.157 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 3
Details: 1 uL drop of 3.4 mg/mL protein in 0.5 M acetic acid, pH 3.0, with 0.12 M magnesium formate, diffraction parameters improved with later addition of 0.1 M sodium bromide, MICROBATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2011
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.693→50 Å / Num. all: 23010 / Num. obs: 23010 / % possible obs: 86 % / 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 3EW1

3ew1


Resolution: 1.693→40.66 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.34 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25972 1159 5 %RANDOM
Rwork0.21229 ---
obs0.21473 21850 85.42 %-
all-21850 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0.16 Å2-1.48 Å2
2---1.02 Å2-1.22 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.693→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 0 135 1779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9172350
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1775214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35122.67671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53915248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.716159
X-RAY DIFFRACTIONr_chiral_restr0.1470.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021339
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.2722
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21149
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0731.51077
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85321700
X-RAY DIFFRACTIONr_scbond_it2.7213773
X-RAY DIFFRACTIONr_scangle_it3.944.5647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.693→1.737 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 72 -
Rwork0.246 1469 -
obs--76.93 %

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