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- PDB-7l5m: Crystal Structure of the DiB-RM-split Protein -

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Basic information

Entry
Database: PDB / ID: 7l5m
TitleCrystal Structure of the DiB-RM-split Protein
Components(Lipocalin family ...) x 2
KeywordsFLUORESCENT PROTEIN / lipocalin / beta barrel / split protein / 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: 2.33 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,6967
Polymers20,1902
Non-polymers5065
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-43 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.146, 57.146, 138.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Lipocalin family ... , 2 types, 2 molecules AB

#1: Protein Lipocalin family protein / DiB-RM-split


Mass: 12285.862 Da / Num. of mol.: 1 / Fragment: N-terminal fragment (UNP residues 20-109) / Mutation: P22S, A36C, F53A, N76F, S89Y, E90V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HGR07_10045, HGR07_25230 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): XJb(DE3) Autolysis / References: UniProt: A0A768MZ64
#2: Protein Lipocalin family protein / DiB-RM-split


Mass: 7903.896 Da / Num. of mol.: 1 / Fragment: C-terminal fragment (UNP residues 110-177) / Mutation: L141N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HGR07_10045, HGR07_25230 / Plasmid: pMRBAD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): XJb(DE3) Autolysis / References: UniProt: A0A768MZ64

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Non-polymers , 4 types, 17 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
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 0.5% 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: Jul 22, 2020
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.33→46.21 Å / Num. obs: 10501 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 49.674 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.087 / Net I/σ(I): 10.9 / Num. measured all: 84479
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
2.33-2.375.31.827815220.2860.697
6.32-46.227.117.844246230.0150.041

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.404
Highest resolutionLowest resolution
Rotation44.1 Å2.72 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: 2.33→44.13 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 501 4.8 %RANDOM
Rwork0.2385 ---
obs0.2404 9939 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.12 Å2 / Biso mean: 55.752 Å2 / Biso min: 33.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0 Å2
2--0.53 Å2-0 Å2
3----1.07 Å2
Refinement stepCycle: final / Resolution: 2.33→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 28 12 1258
Biso mean--94.32 47.46 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131274
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171148
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.6531728
X-RAY DIFFRACTIONr_angle_other_deg2.3441.5852643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1395149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4920.2677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32115196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0181513
X-RAY DIFFRACTIONr_chiral_restr0.0690.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021420
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02311
X-RAY DIFFRACTIONr_mcbond_it4.3495.617602
X-RAY DIFFRACTIONr_mcbond_other4.3485.616601
X-RAY DIFFRACTIONr_mcangle_it6.2538.404749
LS refinement shellResolution: 2.33→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 34 -
Rwork0.383 725 -
all-759 -
obs--99.74 %

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