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- PDB-9rd1: OppA from E. coli in complex with GSisoK -

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Basic information

Entry
Database: PDB / ID: 9rd1
TitleOppA from E. coli in complex with GSisoK
ComponentsPeriplasmic oligopeptide-binding protein OppA
KeywordsTRANSPORT PROTEIN / Substrate recognition specificity / Binding pocket plasticity / Transporter-ligand interactions / Structural basis for selective uptake / Scaffold accommodation
Function / homology
Function and homology information


oligopeptide import across plasma membrane / oligopeptide binding / oligopeptide transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / : / protein transport / outer membrane-bounded periplasmic space / response to heat / membrane
Similarity search - Function
Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle
Similarity search - Domain/homology
: / (R,R)-2,3-BUTANEDIOL / Periplasmic oligopeptide-binding protein OppA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIype, T. / Fottner, M. / Boehm, P. / Piedrafita, C. / Moeller, Y. / Groll, M. / Lang, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1309 Germany
CitationJournal: to be published
Title: Hijacking a bacterial membrane transporter for efficient genetic code expansion
Authors: Iype, T. / Fottner, M. / Boehm, P. / Piedrafita, C. / Moeller, Y. / Groll, M. / Lang, K.
History
DepositionMay 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic oligopeptide-binding protein OppA
B: Periplasmic oligopeptide-binding protein OppA
C: Periplasmic oligopeptide-binding protein OppA
D: Periplasmic oligopeptide-binding protein OppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,00313
Polymers236,4734
Non-polymers1,5309
Water1,60389
1
A: Periplasmic oligopeptide-binding protein OppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4092
Polymers59,1181
Non-polymers2901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic oligopeptide-binding protein OppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4993
Polymers59,1181
Non-polymers3802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Periplasmic oligopeptide-binding protein OppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5334
Polymers59,1181
Non-polymers4143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Periplasmic oligopeptide-binding protein OppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5634
Polymers59,1181
Non-polymers4443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.990, 200.690, 103.380
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Periplasmic oligopeptide-binding protein OppA / Polyamine-induced protein / PI protein


Mass: 59118.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: oppA, b1243, JW1235 / Production host: Escherichia coli (E. coli) / References: UniProt: P23843

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Non-polymers , 5 types, 98 molecules

#2: Chemical
ChemComp-A1JHR / Gly-Ser-epsilon-Lys / (2S)-2-azanyl-6-[[(2S)-2-(2-azanylethanoylamino)-3-oxidanyl-propanoyl]amino]hexanoic acid


Mass: 290.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H22N4O5 / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 15% Ethanol, 40% Pentaerythritol propoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0597 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 80198 / % possible obs: 95.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2 / Num. unique obs: 9241 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.884 / SU B: 31.029 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 4008 5 %RANDOM
Rwork0.22936 ---
obs0.23142 76162 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.32 Å2-0 Å20.08 Å2
2---2.18 Å20 Å2
3----3.1 Å2
Refinement stepCycle: 1 / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16492 0 104 89 16685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01317035
X-RAY DIFFRACTIONr_bond_other_d0.0020.01515850
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.65423217
X-RAY DIFFRACTIONr_angle_other_deg1.0911.59336638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73552064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49523.803852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.488152808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.811568
X-RAY DIFFRACTIONr_chiral_restr0.0380.22222
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023764
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6862.9968268
X-RAY DIFFRACTIONr_mcbond_other0.6852.9968267
X-RAY DIFFRACTIONr_mcangle_it0.9894.49310328
X-RAY DIFFRACTIONr_mcangle_other0.9894.49410329
X-RAY DIFFRACTIONr_scbond_it0.593.058767
X-RAY DIFFRACTIONr_scbond_other0.5913.058768
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8594.52912890
X-RAY DIFFRACTIONr_long_range_B_refined1.47633.95118469
X-RAY DIFFRACTIONr_long_range_B_other1.47433.94918463
X-RAY DIFFRACTIONr_rigid_bond_restr0.23332885
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 303 -
Rwork0.322 5773 -
obs--99.7 %
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)
10.06080.0911-0.05780.5978-0.16120.2294-0.0033-0.03190.0126-0.06650.0070.03140.020.0085-0.00370.0493-0.0115-0.02320.0676-0.00230.0382-7.2762-47.0258-34.3835
20.04920.1299-0.03160.7630.09890.2542-0.003-0.01480.0001-0.03080.0053-0.05610.0199-0.0055-0.00230.0229-0.0002-0.00290.08110.00240.04038.9216-73.613719.0668
30.0759-0.09810.13720.4695-0.09850.2771-0.0010.01080.0195-0.0379-0.0464-0.0752-0.01020.0030.04740.0076-0.01370.00660.10830.00320.064314.7685-22.12510.9665
40.11340.0781-0.08470.27720.01960.21510.0051-0.00820.00270.0819-0.0206-0.03110.00030.00270.01550.03520.0048-0.0260.096-0.00520.043611.60681.891643.7578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 543
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B27 - 543
4X-RAY DIFFRACTION2B601 - 602
5X-RAY DIFFRACTION3C27 - 543
6X-RAY DIFFRACTION3C601 - 603
7X-RAY DIFFRACTION4D27 - 543
8X-RAY DIFFRACTION4D601 - 603

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