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- PDB-9nlt: Crystal Structure of Flpp3-minibinder687 Complex -

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Basic information

Entry
Database: PDB / ID: 9nlt
TitleCrystal Structure of Flpp3-minibinder687 Complex
Components
  • DUF3568 family protein
  • minibinder687
KeywordsAPOPTOSIS / De novo design / deep learning / Plpp3 / minibinder / Francisella-like lipoprotein
Function / homologyLipoprotein Flpp3-like / Protein of unknown function (DUF3568) / Prokaryotic membrane lipoprotein lipid attachment site profile. / IODIDE ION / DUF3568 family protein
Function and homology information
Biological speciesFrancisella tularensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsBera, A.K. / Gokce, G. / Kang, A. / Bhardwaj, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR0011 21 2 0012 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: De Novo Design of High-Affinity Miniprotein Binders Targeting Francisella Tularensis Virulence Factor.
Authors: Gokce-Alpkilic, G. / Huang, B. / Liu, A. / Kreuk, L.S.M. / Wang, Y. / Adebomi, V. / Bueso, Y.F. / Bera, A.K. / Kang, A. / Gerben, S.R. / Rettie, S. / Vafeados, D.K. / Roullier, N. / ...Authors: Gokce-Alpkilic, G. / Huang, B. / Liu, A. / Kreuk, L.S.M. / Wang, Y. / Adebomi, V. / Bueso, Y.F. / Bera, A.K. / Kang, A. / Gerben, S.R. / Rettie, S. / Vafeados, D.K. / Roullier, N. / Goreshnik, I. / Li, X. / Baker, D. / Woodward, J.J. / Mougous, J.D. / Bhardwaj, G.
History
DepositionMar 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DUF3568 family protein
A: minibinder687
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9984
Polymers18,7452
Non-polymers2542
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-10 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.166, 42.891, 54.051
Angle α, β, γ (deg.)90.000, 96.275, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DUF3568 family protein


Mass: 12369.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: DR87_234 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAP6R832
#2: Protein minibinder687


Mass: 6375.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis Tris Propane pH 6.5, 0.2 M Sodium iodide, 20 % w/v PEG 3350 and 10 % v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2025
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.37→35.95 Å / Num. obs: 6471 / % possible obs: 95 % / Redundancy: 6.3 % / Biso Wilson estimate: 25.47 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.327 / Rpim(I) all: 0.212 / Net I/σ(I): 4.3
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.475 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 969 / CC1/2: 0.636 / Rpim(I) all: 0.663 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→35.95 Å / SU ML: 0.3408 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7345
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2688 647 10.02 %
Rwork0.2218 5811 -
obs0.2264 6458 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.57 Å2
Refinement stepCycle: LAST / Resolution: 2.37→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 2 11 1279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221282
X-RAY DIFFRACTIONf_angle_d0.44741725
X-RAY DIFFRACTIONf_chiral_restr0.0399188
X-RAY DIFFRACTIONf_plane_restr0.0033227
X-RAY DIFFRACTIONf_dihedral_angle_d15.6223490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.560.38251340.3331199X-RAY DIFFRACTION99.55
2.56-2.810.32981220.27111098X-RAY DIFFRACTION90.04
2.81-3.220.28951340.23021209X-RAY DIFFRACTION99.85
3.22-4.050.22551180.18571054X-RAY DIFFRACTION85.55
4.06-35.950.22461390.18541251X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 8.79594471967 Å / Origin y: 4.03891414613 Å / Origin z: 16.5260690266 Å
111213212223313233
T0.297976783722 Å2-0.00726159089002 Å2-0.132143737834 Å2-0.210175308666 Å2-0.0138021293715 Å2--0.41536980284 Å2
L3.76252813116 °20.0123434545911 °2-0.429450902549 °2-3.54023782813 °20.122847627042 °2--1.09087528769 °2
S0.162820258995 Å °0.518892612729 Å °-0.442868437484 Å °-0.651360002985 Å °-0.00566763373161 Å °0.438146249271 Å °0.156179668707 Å °-0.143623514033 Å °-0.115850420887 Å °
Refinement TLS groupSelection details: all

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