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- PDB-2jgs: Circular permutant of avidin -

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Basic information

Entry
Database: PDB / ID: 2jgs
TitleCircular permutant of avidin
ComponentsCIRCULAR PERMUTANT OF AVIDIN
KeywordsBIOTIN-BINDING PROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / 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
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaatta, J.A.E. / Hytonen, V.P. / Airenne, T.T. / Niskanen, E. / Johnson, M.S. / Kulomaa, M.S. / Nordlund, H.R.
CitationJournal: Chembiochem / Year: 2008
Title: Rational Modification of Ligand-Binding Preference of Avidin by Circular Permutation and Mutagenesis.
Authors: Maatta, J.A.E. / Airenne, T.T. / Nordlund, H.R. / Janis, J. / Paldanius, T.A. / Vainiotalo, P. / Johnson, M.S. / Kulomaa, M.S. / Hytonen, V.P.
History
DepositionFeb 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 20, 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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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: CIRCULAR PERMUTANT OF AVIDIN
B: CIRCULAR PERMUTANT OF AVIDIN
C: CIRCULAR PERMUTANT OF AVIDIN
D: CIRCULAR PERMUTANT OF AVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2148
Polymers57,2364
Non-polymers9774
Water3,099172
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-90.8 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.768, 79.309, 71.727
Angle α, β, γ (deg.)90.00, 98.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.93877, 0.00881, 0.34443), (0.01252, -0.99989, -0.00854), (0.34432, 0.01233, -0.93877)-16.54458, 1.13228, 91.86986
2given(-0.97379, -0.1691, -0.15214), (-0.1699, 0.09602, 0.98077), (-0.15124, 0.98091, -0.12223)60.36687, -46.2122, 62.29931
3given(-0.97289, 0.15952, -0.16743), (0.15441, -0.0909, -0.98382), (-0.17216, -0.983, 0.0638)61.00995, 47.88213, 53.96689
4given(-0.96731, 0.18693, -0.17138), (0.1572, -0.08833, -0.98361), (-0.19901, -0.97839, 0.05605)61.38431, 47.68832, 54.67527
5given(-0.96965, -0.19465, -0.14797), (-0.16645, 0.0822, 0.98262), (-0.1791, 0.97742, -0.1121)60.38112, -46.48714, 62.13909
6given(0.94743, 0.00547, 0.31993), (0.0078, -0.99995, -0.006), (0.31988, 0.00818, -0.94742)-15.30696, 0.90837, 93.22396

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Components

#1: Protein
CIRCULAR PERMUTANT OF AVIDIN


Mass: 14309.104 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02701*PLUS
#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.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE STRUCTURE DEPOSITED IS A CIRCULAR PERMUTANT (ARTIFICIAL LOCATION OF N- AND C-TERMINI & SHORT ...THE STRUCTURE DEPOSITED IS A CIRCULAR PERMUTANT (ARTIFICIAL LOCATION OF N- AND C-TERMINI & SHORT LINKER REGIONS ETC) OF AVIDIN. HOWEVER, THE SEQUENCE FOR THIS ENGINEERED AVIDIN IS NOT YET DEPOSITED TO E.G. UNIPROT. THERE WILL BE A SEQUENCE ENTRY MATCHING THE DEPOSITED STRUCTURE (EXCEPT THE N76 TO M MUTATION), BUT IT IS NOT YET AVAILABLE. THIS SEQUENCE IS RELATED TO AVIDIN.

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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: 2.21 Å3/Da / Density % sol: 43.95 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 36425 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 1.9→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AVI

2avi


Resolution: 1.9→70.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.01 / SU ML: 0.135 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1818 5 %RANDOM
Rwork0.203 ---
obs0.206 34607 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å2-2 Å2
2---0.48 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 64 172 3764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223700
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9365017
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4075449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29123.567157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27715620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5961524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022726
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22484
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7241.52287
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13223620
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73531631
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.644.51394
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 132
Rwork0.26 2546
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)
12.8906-0.49151.04393.2914-0.81553.2061-0.13850.16820.43520.1493-0.0013-0.0856-0.39880.13850.1398-0.2297-0.05330.054-0.11420.0489-0.052228.6714.53647.56
22.39480.64690.5464.0066-0.33471.73680.2857-0.1608-0.4224-0.0111-0.0775-0.06490.4224-0.0868-0.2082-0.0662-0.0719-0.0854-0.07340.0681-0.053527.368-14.17456.552
32.55810.2931.77532.30160.30334.42950.2186-0.6832-0.0660.4114-0.02560.12190.2235-0.592-0.1931-0.1152-0.09990.01360.060.0508-0.082123.037-2.89166.452
42.4361-0.45120.20972.51890.20653.12970.12820.3813-0.0394-0.31280.0125-0.00890.16630.2163-0.1407-0.21540.00410.043-0.05260.0017-0.111927.7853.68737.568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 130
2X-RAY DIFFRACTION2B1 - 130
3X-RAY DIFFRACTION3C1 - 130
4X-RAY DIFFRACTION4D1 - 130

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