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- PDB-9cdv: Crystal Structure of Rhombotarget A -

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Basic information

Entry
Database: PDB / ID: 9cdv
TitleCrystal Structure of Rhombotarget A
ComponentsRhombotarget A
KeywordsMEMBRANE PROTEIN / De novo design / deep learning / Cyclic Peptide
Biological speciesAcinetobacter terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBera, A.K. / Rettie, S. / Kang, A. / Bhardwaj, G.
Funding support United States, 2items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA) United States
Defense Threat Reduction Agency (DTRA) United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Accurate de novo design of high-affinity protein-binding macrocycles using deep learning.
Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. ...Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. / Murray, A. / Levine, P.M. / Schneider, M. / Vasireddy, V. / Ovchinnikov, S. / Weiergraber, O.H. / Willbold, D. / Kritzer, J.A. / Mougous, J.D. / Baker, D. / DiMaio, F. / Bhardwaj, G.
History
DepositionJun 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhombotarget A
B: Rhombotarget A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4166
Polymers101,1342
Non-polymers2824
Water8,737485
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.156, 106.477, 71.305
Angle α, β, γ (deg.)90.000, 107.040, 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 Rhombotarget A


Mass: 50566.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter terrae (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5 and 20 % (v/v) PEG 5000 MME

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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: 0.72931 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 16, 2023
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: 0.72931 Å / Relative weight: 1
ReflectionResolution: 2→34.1 Å / Num. obs: 55105 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 26.72 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.092 / Net I/σ(I): 6.2
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.61 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4079 / CC1/2: 0.559 / Rpim(I) all: 0.72 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_5288refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.71 Å / SU ML: 0.2417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 2700 4.9 %
Rwork0.1954 52354 -
obs0.1973 55054 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.71 Å2
Refinement stepCycle: LAST / Resolution: 2→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6710 0 17 485 7212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216809
X-RAY DIFFRACTIONf_angle_d0.49869211
X-RAY DIFFRACTIONf_chiral_restr0.04441081
X-RAY DIFFRACTIONf_plane_restr0.00291213
X-RAY DIFFRACTIONf_dihedral_angle_d13.50922491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.34161400.29422788X-RAY DIFFRACTION99.76
2.04-2.080.32511340.29042720X-RAY DIFFRACTION100
2.08-2.120.32261620.28042760X-RAY DIFFRACTION99.97
2.12-2.160.28741320.25522718X-RAY DIFFRACTION99.96
2.16-2.210.27491230.2532787X-RAY DIFFRACTION99.97
2.21-2.270.31911230.23692749X-RAY DIFFRACTION100
2.27-2.330.26081310.24172741X-RAY DIFFRACTION99.9
2.33-2.40.28891590.23752745X-RAY DIFFRACTION99.93
2.4-2.480.281370.22972770X-RAY DIFFRACTION100
2.48-2.570.23591490.21492717X-RAY DIFFRACTION99.9
2.57-2.670.23531400.21372754X-RAY DIFFRACTION100
2.67-2.790.27421390.20722734X-RAY DIFFRACTION100
2.79-2.940.26961550.20852734X-RAY DIFFRACTION99.9
2.94-3.120.22961580.1962777X-RAY DIFFRACTION99.97
3.12-3.360.25141400.18952766X-RAY DIFFRACTION100
3.36-3.70.21851450.17552742X-RAY DIFFRACTION99.93
3.7-4.230.21521330.15392778X-RAY DIFFRACTION100
4.23-5.330.16611480.13882762X-RAY DIFFRACTION99.86
5.33-30.710.16911520.16362812X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 5.74623675518 Å / Origin y: 9.00594902435 Å / Origin z: 17.655714687 Å
111213212223313233
T0.164886554738 Å2-0.0020835043798 Å2-0.00667900666046 Å2-0.155449157848 Å20.0320874204122 Å2--0.182079865042 Å2
L0.284212352329 °2-0.0674096396373 °2-0.159028615804 °2-0.303291232441 °20.249793153017 °2--0.777039968755 °2
S-0.0164785903713 Å °-0.0157623983891 Å °-0.0161548390059 Å °0.0128866268819 Å °0.00235486922729 Å °-0.00776330922757 Å °0.0173988952011 Å °0.035195728206 Å °0.0168892730125 Å °
Refinement TLS groupSelection details: all

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