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- PDB-4bj8: Zebavidin -

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Basic information

Entry
Database: PDB / ID: 4bj8
TitleZebavidin
ComponentsZEBAVIDIN
KeywordsBIOTIN-BINDING PROTEIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAirenne, T.T. / Parthiban, M. / Niederhauser, B. / Zmurko, J. / Kulomaa, M.S. / Hytonen, V.P. / Johnson, M.S.
CitationJournal: Plos One / Year: 2013
Title: Zebavidin
Authors: Niederhauser, B. / Zmurko, J. / Parthiban, M. / Ojanen, M. / Kukkurainen, S. / Maatta, J.A.E. / Leppiniemi, J. / Janis, J. / Parikka, M. / Turpeinen, H. / Pesu, M. / Johnson, M.S. / Airenne, ...Authors: Niederhauser, B. / Zmurko, J. / Parthiban, M. / Ojanen, M. / Kukkurainen, S. / Maatta, J.A.E. / Leppiniemi, J. / Janis, J. / Parikka, M. / Turpeinen, H. / Pesu, M. / Johnson, M.S. / Airenne, T.T. / Kulomaa, M.S. / Hytonen, V.P.
History
DepositionApr 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 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
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. THE SHEETS PRESENTED AS "EA" 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 "FA" 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 "GA" 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 "HA" 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 "IA" 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 "JA" 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 "KA" 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 "LA" 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 "MA" 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 "NA" 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 "OA" 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 "PA" 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

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Assembly

Deposited unit
A: ZEBAVIDIN
B: ZEBAVIDIN
C: ZEBAVIDIN
D: ZEBAVIDIN
E: ZEBAVIDIN
F: ZEBAVIDIN
G: ZEBAVIDIN
H: ZEBAVIDIN
I: ZEBAVIDIN
J: ZEBAVIDIN
K: ZEBAVIDIN
L: ZEBAVIDIN
M: ZEBAVIDIN
N: ZEBAVIDIN
O: ZEBAVIDIN
P: ZEBAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,68533
Polymers217,68416
Non-polymers4,00117
Water9,062503
1
E: ZEBAVIDIN
F: ZEBAVIDIN
G: ZEBAVIDIN
H: ZEBAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3988
Polymers54,4214
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-72.9 kcal/mol
Surface area19350 Å2
MethodPISA
2
A: ZEBAVIDIN
B: ZEBAVIDIN
C: ZEBAVIDIN
D: ZEBAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3988
Polymers54,4214
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-70.9 kcal/mol
Surface area19450 Å2
MethodPISA
3
I: ZEBAVIDIN
J: ZEBAVIDIN
K: ZEBAVIDIN
L: ZEBAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4909
Polymers54,4214
Non-polymers1,0695
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
ΔGint-72.7 kcal/mol
Surface area19650 Å2
MethodPISA
4
M: ZEBAVIDIN
N: ZEBAVIDIN
O: ZEBAVIDIN
P: ZEBAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3988
Polymers54,4214
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-73.7 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.240, 196.840, 52.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
ZEBAVIDIN


Mass: 13605.251 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-A1 / References: UniProt: E7F650
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 16 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE IS LACKING THE RESIDUES 1-30 OF NP_001188371.1, WHICH WERE REPLACED BY AN ...THE CRYSTALLIZED SEQUENCE IS LACKING THE RESIDUES 1-30 OF NP_001188371.1, WHICH WERE REPLACED BY AN OMPA SIGNAL PEPTIDE IN THE EXPRESSION CONSTRUCT. THE TWO FIRST RESIDUES, QT, OF THE CRYSTALLIZED ZEBAVIDIN ARE FROM THE OMPA SIGNAL.

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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: 2.2 Å3/Da / Density % sol: 43 %
Description: TETRAMERIC MODEL OF ZEBAVIDIN WAS DONE USING MODELLER WITHIN THE DISCOVERY STUDIO AND BASED ON WWPDB ENTRY 1WBI.POLY ALAGLY MODEL WAS USED IN MOLECULAR REPLACEMENT.
Crystal growMethod: vapor diffusion, sitting drop
Details: THE PROTEIN SOLUTION (1.6 MG/ML; 50 MM TRIS-HCL. PH 7) WAS MIXED WITH BIOTIN SOLUTION (1 MG/ML; 5 MM TRIS, PH 8.8, 8 MM CHES, PH 9.5) IN 10:1 V/V RATIO BEFORE CRYSTALLIZATION. SITTING DROPS ...Details: THE PROTEIN SOLUTION (1.6 MG/ML; 50 MM TRIS-HCL. PH 7) WAS MIXED WITH BIOTIN SOLUTION (1 MG/ML; 5 MM TRIS, PH 8.8, 8 MM CHES, PH 9.5) IN 10:1 V/V RATIO BEFORE CRYSTALLIZATION. SITTING DROPS WITH 300 NL OF PROTEIN-LIGAND SOLUTION AND 150 NL OF WELL SOLUTION (0.18 M MAGNESIUM CHLORIDE, 0.09 M BIS TRIS, PH 5.5, 23% W/V PEG 3350) WERE USED. 30% V/V GLYCEROL IN WELL SOLUTION WAS ADDED TO THE DROP BEFORE FREEZING IN LIQUID NITROGEN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 74935 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WBI

1wbi


Resolution: 2.4→24.58 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.947 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.592 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26596 3741 5 %RANDOM
Rwork0.19173 ---
obs0.19546 71194 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.233 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2---0.78 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14505 0 262 503 15270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01915232
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214150
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.92820645
X-RAY DIFFRACTIONr_angle_other_deg0.8633.00232425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17651946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8622.556626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.426152441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.13215129
X-RAY DIFFRACTIONr_chiral_restr0.0960.22291
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023788
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.401→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 268 -
Rwork0.226 5129 -
obs--99.45 %

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