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- PDB-4bcs: Crystal structure of an avidin mutant -

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Basic information

Entry
Database: PDB / ID: 4bcs
TitleCrystal structure of an avidin mutant
ComponentsCHIMERIC AVIDIN
KeywordsBIOTIN-BINDING PROTEIN / LIGAND BINDING
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / BIOTIN / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Avidin-related protein 4/5
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAirenne, T.T. / Niederhauser, B. / Hytonen, V.P. / Kulomaa, M.S. / Johnson, M.S.
Citation
Journal: Plos One / Year: 2014
Title: A Novel Chimeric Avidin with Increased Thermal Stability Using DNA Shuffling.
Authors: Taskinen, B. / Airenne, T.T. / Janis, J. / Rahikainen, R. / Johnson, M.S. / Kulomaa, M.S. / Hytonen, V.P.
#1: Journal: J.Biotechnol. / Year: 2012
Title: DNA Family Shuffling within the Chicken Avidin Protein Family - a Shortcut to More Powerful Protein Tools.
Authors: Niederhauser, B. / Siivonen, J. / Maatta, J.A. / Janis, J. / Kulomaa, M.S. / Hytonen, V.P.
History
DepositionOct 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Other
Revision 1.2Apr 30, 2014Group: Database references / Source and taxonomy
Revision 1.3Mar 6, 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 1.4Dec 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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHIMERIC AVIDIN
B: CHIMERIC AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6898
Polymers27,8452
Non-polymers8446
Water2,018112
1
A: CHIMERIC AVIDIN
B: CHIMERIC AVIDIN
hetero molecules

A: CHIMERIC AVIDIN
B: CHIMERIC AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,37816
Polymers55,6914
Non-polymers1,68712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area12420 Å2
ΔGint-89.7 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.110, 47.170, 60.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2031-

HOH

21A-2037-

HOH

31B-2013-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.22495, -0.97432, -0.0098), (-0.97435, -0.225, 0.00449), (-0.00658, 0.00854, -0.99994)
Vector: 63.2223, 78.98196, 47.81317)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CHIMERIC AVIDIN


Mass: 13922.716 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P56734*PLUS

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Non-polymers , 5 types, 118 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsPRODUCED USING A DNA FAMILY SHUFFLING METHOD WITH GENES OF UNIPROT ENTRIES P02701 AND P56734

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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: 2.1 Å3/Da / Density % sol: 41 %
Description: THE POLYPEPTIDE CHAIN A OF 1WBI WAS USED IN MOLECULAR REPLACEMENT.
Crystal growMethod: vapor diffusion
Details: 300 NL OF PROTEIN SOLUTION (7.36 MG PER ML; 50 MM SODIUM ACETATE, PH 4) WERE MIXED WITH 300 NL OF WELL SOLUTION (0.09 M PHOSPHATE, CITRATE, PH 4.2; 36% PEG 300). VAPOUR DIFFUSION WAS USED. ...Details: 300 NL OF PROTEIN SOLUTION (7.36 MG PER ML; 50 MM SODIUM ACETATE, PH 4) WERE MIXED WITH 300 NL OF WELL SOLUTION (0.09 M PHOSPHATE, CITRATE, PH 4.2; 36% PEG 300). VAPOUR DIFFUSION WAS USED. BEFORE CRYSTALLIZATION, BIOTIN SOLUTION (1 MG PER ML; 5 MM TRIS, PH 8.8 AND 8 MM CHES, PH 9.5) WAS ADDED TO THE PROTEIN SOLUTION IN 1 TO 10 (VOLUME PER VOLUME) RATIO, RESPECTIVELY.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 22157 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WBI

1wbi


Resolution: 1.8→19.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.864 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22598 1108 5 %RANDOM
Rwork0.1892 ---
obs0.19105 21049 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.475 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---1.09 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 53 112 2054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021985
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.871.9492692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5185242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09923.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84215327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1681513
X-RAY DIFFRACTIONr_chiral_restr0.1220.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021463
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_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: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 80 -
Rwork0.245 1527 -
obs--100 %

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