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- PDB-1n0s: ENGINEERED LIPOCALIN FLUA IN COMPLEX WITH FLUORESCEIN -

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Basic information

Entry
Database: PDB / ID: 1n0s
TitleENGINEERED LIPOCALIN FLUA IN COMPLEX WITH FLUORESCEIN
ComponentsBilin-binding protein
KeywordsBINDING PROTEIN / PIERIS BRASSICAE / LIPOCALIN / ANTICALIN / PROTEIN ENGINEERING / fluorescein
Function / homology
Function and homology information


pigment binding / response to reactive oxygen species / lipid metabolic process / extracellular region / cytoplasm
Similarity search - Function
Invertebrate colouration protein / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / Bilin-binding protein
Similarity search - Component
Biological speciesPieris brassicae (large cabbage white)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKorndoerfer, I.P. / Skerra, A.
CitationJournal: Proteins / Year: 2003
Title: Crystallographic analysis of an "anticalin" with tailored specificity for fluorescein reveals high structural plasticity of the lipocalin loop region.
Authors: Korndorfer, I.P. / Beste, G. / Skerra, A.
History
DepositionOct 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Swiss-Prot entry P09464 BBP_PIEBR is the sequence of the Bilin-binding protein (BBP) from ...SEQUENCE Swiss-Prot entry P09464 BBP_PIEBR is the sequence of the Bilin-binding protein (BBP) from P. brassicae, from wich this variant was created. Therefore, there are a number of residues which do not match the Swiss-Prot database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bilin-binding protein
B: Bilin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8805
Polymers42,1192
Non-polymers7613
Water1,76598
1
A: Bilin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3922
Polymers21,0591
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bilin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4883
Polymers21,0591
Non-polymers4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.797, 85.039, 66.059
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTYRTYRAA1 - 321 - 32
21ASPASPTYRTYRBB1 - 321 - 32
32LYSLYSTHRTHRAA41 - 4841 - 48
42LYSLYSTHRTHRBB41 - 4841 - 48
53VALVALILEILEAA54 - 6254 - 62
63VALVALILEILEBB54 - 6254 - 62
74TYRTYRASPASPAA67 - 11867 - 118
84TYRTYRASPASPBB67 - 11867 - 118
95LYSLYSSERSERAA121 - 132121 - 132
105LYSLYSSERSERBB121 - 132121 - 132
116THRTHRGLYGLYAA143 - 151143 - 151
126THRTHRGLYGLYBB143 - 151143 - 151
DetailsFluA is a monomer in solution. The crystallographic dimer has probably no physiological relevance.

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Components

#1: Protein Bilin-binding protein / BBP / anticalin flua


Mass: 21059.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pieris brassicae (large cabbage white) / Plasmid: pbbp21-flua / Production host: Escherichia coli (E. coli) / Strain (production host): jm83 / References: UniProt: P09464
#2: Chemical ChemComp-FLU / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / FLUORESCEIN


Mass: 332.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H12O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 2.0 M (NH4)2SO4, 2% (w/v) PEG 400, 10 mM hepes/naoh, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298 KK
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
123 mg/mlprotein1drop
21 mMfluorescein1drop
32.0 Mammonium sulfate1reservoir
42 %(w/v)PEG4001reservoir
510 mMHEPES-NaOH1reservoirpH8.1

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: May 15, 2001 / Details: osmic confocal maxflux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 29552 / Num. obs: 29552 / % possible obs: 95.8 % / Redundancy: 5.39 % / Rsym value: 0.05 / Net I/σ(I): 17.64
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 2.73 / Num. unique all: 2956 / Rsym value: 0.47 / % possible all: 96.1
Reflection
*PLUS
Num. measured all: 79526 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 96.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
EPMRphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kxo

1kxo


Resolution: 2→63.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.365 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24328 1482 5 %RANDOM
Rwork0.19314 ---
obs0.19562 27943 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.125 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.09 Å2
2---0.6 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 55 98 2933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6711.9143984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1470.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022282
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.3979
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.334
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.07221710
X-RAY DIFFRACTIONr_mcangle_it3.45932758
X-RAY DIFFRACTIONr_scbond_it2.45421220
X-RAY DIFFRACTIONr_scangle_it3.85831226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1009 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.35
loose thermal1.3110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 114
Rwork0.244 2068
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 99 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.671

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