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- PDB-6vri: Crystal Structure of the wtBlc-split Protein -

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Basic information

Entry
Database: PDB / ID: 6vri
TitleCrystal Structure of the wtBlc-split Protein
Components(Outer membrane lipoprotein Blc) x 2
KeywordsUNKNOWN FUNCTION / lipocalin / heme / beta barrel / split 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: 1.94 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: Febs Lett. / Year: 2021
Title: Lipocalin Blc is a potential heme-binding protein.
Authors: Bozhanova, N.G. / Calcutt, M.W. / Beavers, W.N. / Brown, B.P. / Skaar, E.P. / Meiler, J.
History
DepositionFeb 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
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

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Assembly

Deposited unit
A: Outer membrane lipoprotein Blc
B: Outer membrane lipoprotein Blc
C: Outer membrane lipoprotein Blc
D: Outer membrane lipoprotein Blc
E: Outer membrane lipoprotein Blc
F: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,37420
Polymers60,5096
Non-polymers1,86514
Water1,29772
1
A: Outer membrane lipoprotein Blc
B: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7468
Polymers20,1702
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-102 kcal/mol
Surface area8460 Å2
MethodPISA
2
C: Outer membrane lipoprotein Blc
D: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3639
Polymers20,1702
Non-polymers1,1937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-75 kcal/mol
Surface area8720 Å2
MethodPISA
3
E: Outer membrane lipoprotein Blc
F: Outer membrane lipoprotein Blc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2663
Polymers20,1702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-45 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.416, 68.416, 217.748
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
11C-303-

HOH

21F-206-

HOH

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Components

#1: Protein Outer membrane lipoprotein Blc


Mass: 12266.708 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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.43 Å3/Da / Density % sol: 49.41 % / Mosaicity: 0.217 °
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 5% w/v n-Dodecyl-b-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.94→59.25 Å / Num. obs: 44856 / % possible obs: 99.5 % / Redundancy: 9 % / Biso Wilson estimate: 30.626 Å2 / Rpim(I) all: 0.051 / Rrim(I) all: 0.15 / Net I/σ(I): 8.1 / Num. measured all: 403082
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1915 / Rpim(I) all: 0.534 / Rrim(I) all: 1.627 / % possible all: 86.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.414
Highest resolutionLowest resolution
Rotation51.81 Å2.22 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QWD

1qwd


Resolution: 1.94→59.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 2141 4.8 %RANDOM
Rwork0.2121 ---
obs0.2139 42637 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.16 Å2 / Biso mean: 32.65 Å2 / Biso min: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å2-0 Å2
2---0.11 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 1.94→59.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 108 72 3887
Biso mean--56.05 29.73 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133909
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173476
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.6745314
X-RAY DIFFRACTIONr_angle_other_deg2.3611.5957991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5165451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37620.38237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1315600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6241539
X-RAY DIFFRACTIONr_chiral_restr0.0780.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024384
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02973
X-RAY DIFFRACTIONr_mcbond_it2.9333.0981822
X-RAY DIFFRACTIONr_mcbond_other2.8953.0971821
X-RAY DIFFRACTIONr_mcangle_it4.0034.6192267
LS refinement shellResolution: 1.94→1.987 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.354 142 -
Rwork0.299 2833 -
obs--90.67 %

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