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- PDB-6ukl: Crystal Structure of a DiB2-split Protein -

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Basic information

Entry
Database: PDB / ID: 6ukl
TitleCrystal Structure of a DiB2-split Protein
Components(Outer membrane lipoprotein ...) x 2
KeywordsFLUORESCENT PROTEIN / lipocalin / beta barrel / split protein / fluorogen activating protein
Function / homology
Function and homology information


response to stress / 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
PROTOPORPHYRIN IX CONTAINING FE / Outer membrane lipoprotein Blc / Outer membrane lipoprotein Blc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsBozhanova, N.G. / Meiler, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM099842 United States
CitationJournal: Sci Rep / Year: 2020
Title: DiB-splits: nature-guided design of a novel fluorescent labeling split system.
Authors: Bozhanova, N.G. / Gavrikov, A.S. / Mishin, A.S. / Meiler, J.
History
DepositionOct 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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
C: Outer membrane lipoprotein Blc
E: Outer membrane lipoprotein Blc
D: Outer membrane lipoprotein Blc
F: Outer membrane lipoprotein Blc
B: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,05324
Polymers60,6056
Non-polymers2,44818
Water1,910106
1
A: Outer membrane lipoprotein Blc
B: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8749
Polymers20,2022
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-95 kcal/mol
Surface area8700 Å2
MethodPISA
2
C: Outer membrane lipoprotein Blc
D: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,16910
Polymers20,2022
Non-polymers9678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-81 kcal/mol
Surface area8670 Å2
MethodPISA
3
E: Outer membrane lipoprotein Blc
F: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0105
Polymers20,2022
Non-polymers8093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-58 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.241, 68.241, 216.292
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11F-211-

HOH

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Components

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Outer membrane lipoprotein ... , 2 types, 6 molecules ACEDFB

#1: Protein Outer membrane lipoprotein Blc


Mass: 12298.773 Da / Num. of mol.: 3 / Fragment: N-terminal fragment (UNP residues 23-109)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blc, Z5756, ECs5130 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): XJb(DE3) Autolysis / References: UniProt: P0A902, UniProt: P0A901*PLUS
#2: Protein Outer membrane lipoprotein Blc


Mass: 7902.951 Da / Num. of mol.: 3 / Fragment: C-terminal fragment (UNP residues 110-177)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blc, Z5756, ECs5130 / Plasmid: pMRBAD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): XJb(DE3) Autolysis / References: UniProt: P0A902, UniProt: P0A901*PLUS

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Non-polymers , 4 types, 124 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.6 M ammonium sulfate, 0.1 M MES, pH 4.5, supplemented with 10% 0.1 M iron(III) chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.02→72.1 Å / Num. obs: 39425 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 30.423 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.099 / Net I/σ(I): 11.5 / Num. measured all: 346459
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1913 / Rpim(I) all: 0.335 / Rrim(I) all: 0.989 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QWD

1qwd


Resolution: 2.02→72.1 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 1885 4.8 %RANDOM
Rwork0.2051 ---
obs0.2071 37418 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.69 Å2 / Biso mean: 36.833 Å2 / Biso min: 19.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 2.02→72.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 142 106 3946
Biso mean--69.57 36.06 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133938
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173496
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.6735355
X-RAY DIFFRACTIONr_angle_other_deg2.3371.5968052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4945454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.99720.383235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60415603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8051539
X-RAY DIFFRACTIONr_chiral_restr0.0820.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024384
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02965
X-RAY DIFFRACTIONr_mcbond_it3.2123.491828
X-RAY DIFFRACTIONr_mcbond_other3.2143.4861826
X-RAY DIFFRACTIONr_mcangle_it4.2845.2082275
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 151 -
Rwork0.262 2701 -
all-2852 -
obs--97.94 %

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