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- PDB-3tcf: Crystal structure of E. coli OppA complexed with endogenous ligands -

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Basic information

Entry
Database: PDB / ID: 3tcf
TitleCrystal structure of E. coli OppA complexed with endogenous ligands
Components
  • Endogenous peptide
  • Periplasmic oligopeptide-binding protein
KeywordsPROTEIN TRANSPORT / Peptide-binding protein / peptide transport / ABC transporter
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 / chaperone-mediated protein folding / protein transport / outer membrane-bounded periplasmic space / response to heat / membrane
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / 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 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKlepsch, M.M. / Kovermann, M. / Low, C. / Balbach, J. / de Gier, J.W. / Slotboom, D.J. / Berntsson, R.P.-A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Escherichia coli peptide binding protein OppA has a preference for positively charged peptides.
Authors: Klepsch, M.M. / Kovermann, M. / Low, C. / Balbach, J. / Permentier, H.P. / Fusetti, F. / de Gier, J.W. / Slotboom, D.J. / Berntsson, R.P.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic oligopeptide-binding protein
B: Periplasmic oligopeptide-binding protein
C: Periplasmic oligopeptide-binding protein
D: Periplasmic oligopeptide-binding protein
E: Periplasmic oligopeptide-binding protein
F: Periplasmic oligopeptide-binding protein
G: Periplasmic oligopeptide-binding protein
H: Periplasmic oligopeptide-binding protein
I: Endogenous peptide
J: Endogenous peptide
K: Endogenous peptide
L: Endogenous peptide
M: Endogenous peptide
N: Endogenous peptide
O: Endogenous peptide
P: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)477,28816
Polymers477,28816
Non-polymers00
Water43,3802408
1
A: Periplasmic oligopeptide-binding protein
I: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)59,6612
Polymers59,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-4 kcal/mol
Surface area20740 Å2
MethodPISA
2
B: Periplasmic oligopeptide-binding protein
J: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)59,6612
Polymers59,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-3 kcal/mol
Surface area20540 Å2
MethodPISA
3
C: Periplasmic oligopeptide-binding protein
K: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)59,6612
Polymers59,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-3 kcal/mol
Surface area20720 Å2
MethodPISA
4
D: Periplasmic oligopeptide-binding protein
L: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)59,6612
Polymers59,6612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-3 kcal/mol
Surface area20740 Å2
MethodPISA
5
E: Periplasmic oligopeptide-binding protein
M: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)59,6612
Polymers59,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-4 kcal/mol
Surface area20670 Å2
MethodPISA
6
F: Periplasmic oligopeptide-binding protein
N: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)59,6612
Polymers59,6612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-3 kcal/mol
Surface area20500 Å2
MethodPISA
7
G: Periplasmic oligopeptide-binding protein
O: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)59,6612
Polymers59,6612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-3 kcal/mol
Surface area20720 Å2
MethodPISA
8
H: Periplasmic oligopeptide-binding protein
P: Endogenous peptide


Theoretical massNumber of molelcules
Total (without water)59,6612
Polymers59,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-3 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.619, 202.599, 208.947
Angle α, β, γ (deg.)90.000, 95.710, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTHE PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN HAS BEEN VERIFIED TO BE A MONOMER BY GEL FILTRATION AND LIGHT SCATTERING

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Components

#1: Protein
Periplasmic oligopeptide-binding protein


Mass: 59387.629 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1243, JW1235, oppA / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23843
#2: Protein/peptide
Endogenous peptide


Mass: 273.330 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2408 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMOLECULE-2 IS AN ENDOGENOUSLY CO-PURIFIED PEPTIDE. THE RESIDUES IN THESE CHAINS HAVE BEEN MODELED AS ALANINES

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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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, glycerol, pH 6.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.972 Å
DetectorDetector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 345441 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.543 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.41
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.120.5542.2618337753085194.2
2.12-2.260.3543.6919529652829199.7
2.26-2.440.2595.0718700549270199.9
2.44-2.680.1737.4317409945338199.9
2.68-2.990.10611.5915891941163199.9
2.99-3.450.06119.2213975836189199.9
3.45-4.220.03929.6111786130701199.9
4.22-5.950.03135.279162223801199.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.37 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.2303 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8101 / SU B: 10.022 / SU ML: 0.15 / SU R Cruickshank DPI: 0.1979 / SU Rfree: 0.1719 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 17271 5 %RANDOM
Rwork0.2287 ---
obs0.2306 345407 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.19 Å2 / Biso mean: 29.9819 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.01 Å2
2---0.26 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33104 0 0 2408 35512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02234092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0222664
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9546524
X-RAY DIFFRACTIONr_angle_other_deg0.9153.00155558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02954176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10224.9781563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.481155623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.54115136
X-RAY DIFFRACTIONr_chiral_restr0.0790.25122
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02137865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026643
LS refinement shellResolution: 2→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 1135 -
Rwork0.323 21490 -
all-22625 -
obs--88.55 %
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)
10.4565-0.21030.14310.8693-0.21650.6945-0.01240.02560.0186-0.0273-0.0196-0.19430.01570.10360.0320.00490.0089-0.01380.2089-0.01880.205113.8458-22.271512.0018
20.4784-0.1310.13991.4791-0.1860.6306-0.01230.0241-0.0248-0.1298-0.0455-0.3778-0.03350.1040.05780.1597-0.02560.06780.1795-0.01390.22314.4554-22.2779114.5117
30.2720.2145-0.04731.99920.45330.8208-0.0471-0.0090.00140.10030.0655-0.13920.13920.0552-0.01840.20720.02250.0070.18340.00790.13227.9716-74.121919.6421
40.3196-0.2387-0.01031.7211-0.37410.90870.00970.02350.0275-0.01760.00230.2060.143-0.0447-0.01210.214-0.010.00920.1801-0.02010.1763-20.895127.120185.0627
50.27130.2488-0.01061.4048-0.33730.87210.0380.0141-0.03110.11750.00890.1404-0.0962-0.0526-0.0470.10050.0413-0.00270.1895-0.01340.1621-19.6938-47.555669.7484
60.53510.1769-0.09150.9955-0.220.639-0.0118-0.04890.02650.2039-0.0398-0.18740.010.09390.05150.09110.0322-0.03870.2153-0.01010.18989.14362.041544.6605
70.5283-0.2089-0.1091.3967-0.02440.6481-0.02020.07160.0101-0.2943-0.0280.25150.1811-0.10950.04820.2154-0.0205-0.02890.21530.01350.1834-23.8629-99.332160.6056
80.2606-0.29460.04973.46260.04450.94270.0537-0.0533-0.01410.508-0.0399-0.1092-0.04950.0181-0.01380.3051-0.0326-0.00740.20980.01370.19264.983253.918235.1068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 3304
2X-RAY DIFFRACTION2B27 - 3283
3X-RAY DIFFRACTION3C13 - 3306
4X-RAY DIFFRACTION4D11 - 3300
5X-RAY DIFFRACTION5E2 - 3305
6X-RAY DIFFRACTION6F3 - 3294
7X-RAY DIFFRACTION7G1 - 3301
8X-RAY DIFFRACTION8H24 - 3307

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