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- PDB-4bbo: Crystal structure of core-bradavidin -

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Basic information

Entry
Database: PDB / ID: 4bbo
TitleCrystal structure of core-bradavidin
ComponentsBLR5658 PROTEIN
KeywordsBIOTIN-BINDING PROTEIN / AVIDINS
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
ACETATE ION / BIOTIN / Blr5658 protein
Similarity search - Component
Biological speciesBRADYRHIZOBIUM JAPONICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAirenne, T.T. / Johnson, M.S. / Maatta, J.A.E. / Hytonen, V.H. / Kulomaa, M.S.
CitationJournal: To be Published
Title: Crystal Structure of Core-Bradavidin
Authors: Airenne, T.T. / Maatta, J.A.E. / Nordlund, H. / Kulomaa, M.S. / Johnson, M.S.
History
DepositionSep 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BLR5658 PROTEIN
B: BLR5658 PROTEIN
C: BLR5658 PROTEIN
D: BLR5658 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,44712
Polymers49,2014
Non-polymers1,2468
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-48.9 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.946, 78.647, 100.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.79512, 0.60643, -0.00525), (0.60638, -0.79513, -0.00861), (-0.0094, 0.00366, -0.99995)5.51383, -16.66453, -25.09087
2given(-0.81874, -0.53638, -0.20484), (-0.5162, 0.53143, 0.67166), (-0.25141, 0.65565, -0.71198)83.37444, 34.93614, -14.56345
3given(-0.96555, -0.09964, 0.2404), (-0.08414, -0.75463, -0.65074), (0.24625, -0.64854, 0.72024)93.25267, 6.2011, -10.77602
4given(-0.97518, -0.06892, 0.2104), (-0.091, -0.74156, -0.66468), (0.20183, -0.66733, 0.71689)92.90064, 6.3882, -8.83114
5given(-0.82923, -0.50855, -0.23186), (-0.52151, 0.55481, 0.64824), (-0.20102, 0.65845, -0.72528)83.53468, 34.59206, -16.89169
6given(0.79462, 0.60709, 0.00519), (0.60711, -0.79453, -0.01174), (-0.003, 0.01248, -0.99992)5.85409, -16.83226, -25.5683

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Components

#1: Protein
BLR5658 PROTEIN / BRADAVIDIN


Mass: 12300.226 Da / Num. of mol.: 4 / Fragment: RESIDUES 26-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRADYRHIZOBIUM JAPONICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q89IH6
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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 Å3/Da / Density % sol: 38.68 %
Description: CORE REGION OF 2Y32 WAS USED FOR MOLECULAR REPLACEMENT.
Crystal growMethod: vapor diffusion, hanging drop
Details: ONE MICROLITER OF THE PROTEIN SOLUTION (LESS THAN 1 MG PER ML AND IN 50 MM SODIUM ACETATE, 100 MM NACL, PH 4) WAS CRYSTALLIZED BY ADDING ONE MICROLITER OF THE WELL SOLUTION (0.1 M HEPES PH 7. ...Details: ONE MICROLITER OF THE PROTEIN SOLUTION (LESS THAN 1 MG PER ML AND IN 50 MM SODIUM ACETATE, 100 MM NACL, PH 4) WAS CRYSTALLIZED BY ADDING ONE MICROLITER OF THE WELL SOLUTION (0.1 M HEPES PH 7.4, 0.8 M K,NA TARTRATE).HANGING DROPS AND VAPOUR DIFFUSION METHOD WAS USED AT RT. BEFORE CRYSTALLIZATION, 25 MICROLITERS OF THE PROTEIN SAMPLE WAS INCUBATED WITH 1 MICRO LITER OF BIOTIN SOLUTION (1 MG PER ML AND IN 5 MM TRIS PH 8.8, 8 MM CHES PH 9.5) FOR 3.5 HOURS AT 37 DEGREES OF CELCIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.063
DetectorDate: Apr 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.063 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 52798 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y32

2y32


Resolution: 1.6→61.9 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.959 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17863 2690 5.1 %RANDOM
Rwork0.14685 ---
obs0.14843 50108 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.577 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.78 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→61.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 82 368 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213569
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.8964924
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96925.733150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9215437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022776
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6261.52237
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22423571
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.83831332
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7154.51337
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 211 -
Rwork0.22 3640 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.51020.0159-0.25430.793-0.05670.73750.0007-0.0471-0.00150.0514-0.0079-0.04970.0080.00850.00720.0512-0.0014-0.00690.11070.00060.076743.0327.4862.444
20.3006-0.1611-0.03590.75360.22071.1648-0.02980.0163-0.0047-0.0802-0.0015-0.02090.0386-0.02610.03130.0655-0.00450.00640.1102-0.00270.0844.3843.309-28.142
30.8153-0.2424-0.19941.3840.35391.089-0.0015-0.00050.0773-0.1381-0.0110.0177-0.1827-0.03970.01260.08810.00050.00640.1069-0.00560.082443.69918.258-22.197
40.54480.0271-0.15860.94650.01691.0075-0.0549-0.0423-0.1062-0.0244-0.0163-0.12150.16010.11120.07120.06970.01660.00470.12520.00620.108851.635-4.322-3.533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2B1 - 120
3X-RAY DIFFRACTION3C1 - 120
4X-RAY DIFFRACTION4D3 - 120

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