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- PDB-6ubo: Fluorogen Activating Protein Dib1 -

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Basic information

Entry
Database: PDB / ID: 6ubo
TitleFluorogen Activating Protein Dib1
ComponentsOuter membrane lipoprotein Blc
KeywordsTRANSPORT PROTEIN / FLUOROGEN ACTIVATING PROTEIN / LIPOCALIN / BIOMARKER / MEMBRANE PROTEIN
Function / homology
Function and homology information


cell outer membrane / lipid binding / DNA damage response
Similarity search - Function
Lipocalin, bacterial / : / Lipocalin-like domain / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipocalin signature.
Similarity search - Domain/homology
CITRIC ACID / polyethylene glycol / Chem-Q3J / Outer membrane lipoprotein Blc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsMuslinkina, L. / Pletneva, N. / Pletnev, V.Z. / Pletnev, S.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structure-Based Rational Design of Two Enhanced Bacterial Lipocalin Blc Tags for Protein-PAINT Super-resolution Microscopy.
Authors: Muslinkina, L. / Gavrikov, A.S. / Bozhanova, N.G. / Mishin, A.S. / Baranov, M.S. / Meiler, J. / Pletneva, N.V. / Pletnev, V.Z. / Pletnev, S.
History
DepositionSep 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane lipoprotein Blc
B: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7438
Polymers40,3952
Non-polymers2,3486
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-14 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.843, 44.843, 158.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Outer membrane lipoprotein Blc


Mass: 20197.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: blc, yjeL, b4149, JW4110 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A901
#2: Chemical ChemComp-Q3J / 12-(diethylamino)-2,2-bis(fluoranyl)-4,5-dimethyl-5-aza-3-azonia-2-boranuidatricyclo[7.4.0.0^{3,7}]trideca-1(13),3,7,9,11-pentaen-6-one


Mass: 319.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20BF2N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol / Polyethylene glycol


Mass: 662.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H62O15
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Na citrate pH 5.0, 30% PEG 550MME, 0.2M NaSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 42279 / % possible obs: 99 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Χ2: 0.922 / Net I/σ(I): 11.4 / Num. measured all: 321104
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.647.40.46941810.8930.1830.5040.77897.9
1.64-1.77.60.36241930.9340.1390.3880.80198.3
1.7-1.787.60.2641800.9670.10.2780.82698.6
1.78-1.877.60.17542340.9840.0670.1870.85598.8
1.87-1.997.60.1242040.9930.0460.1280.9499
1.99-2.147.60.08742250.9960.0340.0930.99699.2
2.14-2.367.60.06942480.9970.0270.0740.9999.4
2.36-2.77.60.05242270.9980.020.0551.0299.5
2.7-3.47.60.0442730.9990.0150.0430.98299.7
3.4-507.60.025431410.010.0261.01699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.25data extraction
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QWD

1qwd


Resolution: 1.58→31.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.581 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0841 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1317 3.1 %RANDOM
Rwork0.1632 ---
obs0.1644 40941 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62.86 Å2 / Biso mean: 20.032 Å2 / Biso min: 9.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.17 Å2
Refinement stepCycle: final / Resolution: 1.58→31.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 109 231 2898
Biso mean--31.51 28.42 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192847
X-RAY DIFFRACTIONr_bond_other_d0.0020.022607
X-RAY DIFFRACTIONr_angle_refined_deg2.3941.9723860
X-RAY DIFFRACTIONr_angle_other_deg0.97335984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26122.394142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32915441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3171530
X-RAY DIFFRACTIONr_chiral_restr0.2110.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
LS refinement shellResolution: 1.58→1.62 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.215 91 -
Rwork0.199 2981 -
obs--97.87 %

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