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- PDB-7l5k: Crystal structure of the DiB-RM protein -

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Basic information

Entry
Database: PDB / ID: 7l5k
TitleCrystal structure of the DiB-RM protein
ComponentsLipocalin family protein
KeywordsFLUORESCENT PROTEIN / lipocalin / beta barrel / fluorogen activating protein / designed protein
Function / homologyISOPROPYL ALCOHOL / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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)43,80522
Polymers40,3692
Non-polymers3,43620
Water3,045169
1
A: Lipocalin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,80610
Polymers20,1851
Non-polymers1,6229
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipocalin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,99912
Polymers20,1851
Non-polymers1,81411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.256, 69.256, 80.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulfate, 2.5% 2-propanol, 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: Aug 17, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.86→33.32 Å / Num. obs: 36055 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.517 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.077 / Net I/σ(I): 9.1 / Num. measured all: 148895
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.86-1.893.92690517760.2260.46998.7
5.04-33.334.115.3734517840.0280.05798.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.354
Highest resolutionLowest resolution
Rotation33.33 Å2.25 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOLREPphasing
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QWD

1qwd


Resolution: 1.86→33.32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 1763 4.9 %RANDOM
Rwork0.1803 ---
obs0.1823 34256 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.26 Å2 / Biso mean: 38.022 Å2 / Biso min: 24.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: final / Resolution: 1.86→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 138 169 2835
Biso mean--64.8 43.1 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132726
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172463
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.6753684
X-RAY DIFFRACTIONr_angle_other_deg2.3041.6435678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5235316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.03620.581155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0071524
X-RAY DIFFRACTIONr_chiral_restr0.080.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022983
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02645
X-RAY DIFFRACTIONr_mcbond_it3.0483.7921264
X-RAY DIFFRACTIONr_mcbond_other3.0483.7911263
X-RAY DIFFRACTIONr_mcangle_it3.8035.6731577
LS refinement shellResolution: 1.86→1.908 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 138 -
Rwork0.266 2453 -
all-2591 -
obs--99.01 %

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