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- PDB-7l5l: Crystal structure of the DiB-RM protein -

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Basic information

Entry
Database: PDB / ID: 7l5l
TitleCrystal structure of the DiB-RM protein
ComponentsLipocalin family protein
KeywordsFLUORESCENT PROTEIN / lipocalin / beta barrel / fluorogen activating protein / designed protein
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsBozhanova, N.G. / Harp, J.M. / 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: Plos Comput.Biol. / Year: 2021
Title: Computational redesign of a fluorogen activating protein with Rosetta.
Authors: Bozhanova, N.G. / Harp, J.M. / Bender, B.J. / Gavrikov, A.S. / Gorbachev, D.A. / Baranov, M.S. / Mercado, C.B. / Zhang, X. / Lukyanov, K.A. / Mishin, A.S. / Meiler, J.
History
DepositionDec 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipocalin family protein
B: Lipocalin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5624
Polymers40,3692
Non-polymers1922
Water2,198122
1
A: Lipocalin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2812
Polymers20,1851
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipocalin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2812
Polymers20,1851
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.970, 44.970, 158.650
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 Lipocalin family protein / DiB-RM


Mass: 20184.699 Da / Num. of mol.: 2 / Fragment: UNP residues 20-177 / Mutation: P22S, A36C, F53A, N76F, S89Y, E90V, L141N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HGR07_10045, HGR07_25230 / Plasmid: pBad / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): XJb(DE3) Autolysis / References: UniProt: A0A768MZ64
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.09 % / Mosaicity: 0.121 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M lithium sulfate, 5% isopropanol, 0.1 M cesium chloride

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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: Jun 20, 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: 2.01→39.12 Å / Num. obs: 20728 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 23.874 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.095 / Net I/σ(I): 12.9 / Num. measured all: 106493
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.01-2.0451.6533910630.461.09799.7
5.45-39.135.135.6526910370.0140.03497.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.56
Highest resolutionLowest resolution
Rotation39.12 Å2.21 Å

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Processing

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

1qwd


Resolution: 2.01→39.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.467 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 906 4.4 %RANDOM
Rwork0.1914 ---
obs0.1933 19768 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.25 Å2 / Biso mean: 31.536 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.01→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 10 122 2654
Biso mean--69.12 31.09 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122615
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172343
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6553555
X-RAY DIFFRACTIONr_angle_other_deg1.2351.585399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.76520.253158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84915402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6131526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
X-RAY DIFFRACTIONr_mcbond_it2.1793.141256
X-RAY DIFFRACTIONr_mcbond_other2.1723.1381254
X-RAY DIFFRACTIONr_mcangle_it2.9814.6971568
LS refinement shellResolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 62 -
Rwork0.267 1468 -
all-1530 -
obs--99.48 %

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