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- PDB-9cdu: Crystal Structure of Rhombotarget A-peptide Complex -

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Basic information

Entry
Database: PDB / ID: 9cdu
TitleCrystal Structure of Rhombotarget A-peptide Complex
Components
  • RBB_D10 peptide
  • Rhombotarget A
KeywordsMEMBRANE PROTEIN / De novo design / deep learning / Cyclic peptide
Biological speciesAcinetobacter terrae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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: RBB_D10 peptide
C: Rhombotarget A
D: RBB_D10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1478
Polymers104,3704
Non-polymers7774
Water1,38777
1
A: Rhombotarget A
B: RBB_D10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7675
Polymers52,1852
Non-polymers5833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-9 kcal/mol
Surface area18450 Å2
MethodPISA
2
C: Rhombotarget A
D: RBB_D10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3793
Polymers52,1852
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-7 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.778, 169.837, 59.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,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: Protein/peptide RBB_D10 peptide


Mass: 1617.818 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5 and 40 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 28, 2024 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.61→34.56 Å / Num. obs: 32591 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 58.62 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.088 / Net I/σ(I): 6.6
Reflection shellResolution: 2.61→2.75 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1 / Num. unique obs: 4662 / CC1/2: 0.409 / Rpim(I) all: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_5246refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→34.56 Å / SU ML: 0.3543 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2587 2000 6.15 %
Rwork0.2123 30541 -
obs0.2151 32541 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.34 Å2
Refinement stepCycle: LAST / Resolution: 2.61→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6774 0 49 78 6901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00186904
X-RAY DIFFRACTIONf_angle_d0.47559322
X-RAY DIFFRACTIONf_chiral_restr0.04221085
X-RAY DIFFRACTIONf_plane_restr0.00491227
X-RAY DIFFRACTIONf_dihedral_angle_d14.15622546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.670.3861400.31982135X-RAY DIFFRACTION100
2.67-2.740.35421390.30862128X-RAY DIFFRACTION100
2.74-2.820.31691420.28522168X-RAY DIFFRACTION100
2.82-2.920.37321400.28022139X-RAY DIFFRACTION100
2.92-3.020.34921420.2662166X-RAY DIFFRACTION99.91
3.02-3.140.27451430.24722179X-RAY DIFFRACTION99.96
3.14-3.280.26081400.22222151X-RAY DIFFRACTION99.96
3.28-3.460.23881420.20532159X-RAY DIFFRACTION99.91
3.46-3.670.25651420.19662170X-RAY DIFFRACTION99.83
3.67-3.960.23711430.19662188X-RAY DIFFRACTION99.79
3.96-4.350.23151420.18132174X-RAY DIFFRACTION99.74
4.35-4.980.20791450.16542203X-RAY DIFFRACTION99.62
4.98-6.270.25631450.21912229X-RAY DIFFRACTION99.71
6.27-34.560.25171550.20822352X-RAY DIFFRACTION99.84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.842574671080.6019113969971.359259980441.23637221980.8476050255631.818471913640.0448677472284-0.1009481934730.1239246025180.0566132845074-0.1164738577030.141162394082-0.0135898994685-0.1362864635520.07134959247090.3346865662080.00882824100610.05648861187560.312808854863-0.02576410346770.3017448447918.01730.658.389
22.982365220883.584609994741.261076595724.650579923132.48121918523.258164584780.0113592380716-0.6617355282530.0815314238416-0.465419085633-0.5796817428730.2692257964360.230532290468-0.4318623862480.5043231135440.843155449378-0.0538591447916-0.007500061691110.629452891108-0.03567326721230.7911348261083.12841.92617.998
34.291946224390.0518963617787-1.509138447825.840349689770.2244277909183.86926423174-0.412062937505-0.113999277740.27285870055-0.0497422780282-0.156098633896-1.02897101389-0.7105116573710.5578622034320.5146483950131.06562587499-0.273566189767-0.2074810545830.7643911633210.2227340104280.87713662719940.23135.079-21.579
42.158246146361.20258793111-0.2218830658370.919090589629-0.09835531360911.254393094860.0974298858244-0.1922667045440.127037161461-0.3312750227670.498175878294-0.38518711418-0.4784684609681.0530053854-0.5599538037481.30246389185-0.2277057577390.2223187244341.869484922390.09943797221891.4392021169241.6885.16-28.267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:443 )A2 - 443
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:14 )B2 - 14
3X-RAY DIFFRACTION3( CHAIN C AND RESID 2:14 )C2 - 14
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:14 )D1 - 14

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