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- PDB-3tcg: Crystal structure of E. coli OppA complexed with the tripeptide KGE -

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Basic information

Entry
Database: PDB / ID: 3tcg
TitleCrystal structure of E. coli OppA complexed with the tripeptide KGE
Components
  • KGE Peptide
  • Periplasmic oligopeptide-binding protein
KeywordsPROTEIN TRANSPORT / peptide-binding domain / Peptide-binding protein / peptide transport / ABC transporter
Function / homology
Function and homology information


oligopeptide import across plasma membrane / oligopeptide binding / oligopeptide transport / peptide transmembrane transporter activity / peptide transport / 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 OppA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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: Advisory / Author supporting evidence
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Nov 27, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: KGE Peptide
J: KGE Peptide
K: KGE Peptide
L: KGE Peptide
M: KGE Peptide
N: KGE Peptide
O: KGE Peptide
P: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)477,76816
Polymers477,76816
Non-polymers00
Water53,3062959
1
A: Periplasmic oligopeptide-binding protein
I: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)59,7212
Polymers59,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-1 kcal/mol
Surface area20320 Å2
MethodPISA
2
B: Periplasmic oligopeptide-binding protein
J: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)59,7212
Polymers59,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint0 kcal/mol
Surface area20300 Å2
MethodPISA
3
C: Periplasmic oligopeptide-binding protein
K: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)59,7212
Polymers59,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint0 kcal/mol
Surface area20320 Å2
MethodPISA
4
D: Periplasmic oligopeptide-binding protein
L: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)59,7212
Polymers59,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-1 kcal/mol
Surface area20240 Å2
MethodPISA
5
E: Periplasmic oligopeptide-binding protein
M: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)59,7212
Polymers59,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-0 kcal/mol
Surface area20420 Å2
MethodPISA
6
F: Periplasmic oligopeptide-binding protein
N: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)59,7212
Polymers59,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-0 kcal/mol
Surface area20140 Å2
MethodPISA
7
G: Periplasmic oligopeptide-binding protein
O: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)59,7212
Polymers59,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-1 kcal/mol
Surface area20270 Å2
MethodPISA
8
H: Periplasmic oligopeptide-binding protein
P: KGE Peptide


Theoretical massNumber of molelcules
Total (without water)59,7212
Polymers59,7212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-1 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.487, 201.308, 206.947
Angle α, β, γ (deg.)90.000, 95.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12I
22J
32K
42L
52M
62N
72O
82P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 517
2116B1 - 517
3116C1 - 517
4116D1 - 517
5116E1 - 517
6116F1 - 517
7116G1 - 517
8116H1 - 517
1124I1 - 3
2124J1 - 3
3124K1 - 3
4124L1 - 3
5124M1 - 3
6124N1 - 3
7124O1 - 3
8124P1 - 3

NCS ensembles :
ID
1
2
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
KGE Peptide


Mass: 333.361 Da / Num. of mol.: 8 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2959 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.64 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorDetector: CCD / Date: Feb 26, 2010
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: 341284 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.976 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.120.5742.5720051253975197.5
2.12-2.260.3863.7919651052027199.9
2.26-2.440.2755.0218341548402199.9
2.44-2.680.1897.0916878644537199.9
2.68-2.990.12110.3515234040353199.8
2.99-3.450.07615.4713334635563199.6
3.45-4.220.05121.7511094330018199.6
4.22-5.950.04225.368471323327199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.36 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.89 Å
Translation2.5 Å48.89 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.89 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.1865 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8517 / SU B: 8.45 / SU ML: 0.127 / SU R Cruickshank DPI: 0.1827 / SU Rfree: 0.1667 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 17050 5 %RANDOM
Rwork0.1992 ---
obs0.2015 340991 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.76 Å2 / Biso mean: 25.062 Å2 / Biso min: 7.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33160 0 0 2959 36119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02234200
X-RAY DIFFRACTIONr_bond_other_d0.0010.0222799
X-RAY DIFFRACTIONr_angle_refined_deg1.171.95146657
X-RAY DIFFRACTIONr_angle_other_deg0.8493.00155883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58154178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64524.9871576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.794155675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.26615136
X-RAY DIFFRACTIONr_chiral_restr0.0690.25114
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02137982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026666
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A6889LOOSE POSITIONAL0.345
1B6889LOOSE POSITIONAL0.325
1C6889LOOSE POSITIONAL0.315
1D6889LOOSE POSITIONAL0.295
1E6889LOOSE POSITIONAL0.335
1F6889LOOSE POSITIONAL0.315
1G6889LOOSE POSITIONAL0.335
1H6889LOOSE POSITIONAL0.375
1A6889LOOSE THERMAL1.8510
1B6889LOOSE THERMAL1.4210
1C6889LOOSE THERMAL1.4210
1D6889LOOSE THERMAL1.3710
1E6889LOOSE THERMAL1.5910
1F6889LOOSE THERMAL1.4210
1G6889LOOSE THERMAL1.3410
1H6889LOOSE THERMAL2.510
2I40MEDIUM POSITIONAL0.80.5
2J40MEDIUM POSITIONAL0.80.5
2K40MEDIUM POSITIONAL0.810.5
2L40MEDIUM POSITIONAL0.850.5
2M40MEDIUM POSITIONAL0.770.5
2N40MEDIUM POSITIONAL0.860.5
2O40MEDIUM POSITIONAL0.790.5
2P40MEDIUM POSITIONAL0.760.5
2I40MEDIUM THERMAL1.682
2J40MEDIUM THERMAL2.222
2K40MEDIUM THERMAL2.162
2L40MEDIUM THERMAL2.292
2M40MEDIUM THERMAL1.952
2N40MEDIUM THERMAL2.62
2O40MEDIUM THERMAL0.762
2P40MEDIUM THERMAL3.492
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 1238 -
Rwork0.287 23536 -
all-24774 -
obs--99.39 %
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)
10.4857-0.23050.1540.7807-0.21080.6416-0.01820.03910.00590.0076-0.0315-0.1138-0.00540.07870.04970.00860.0007-0.01780.0891-0.00940.060613.829-22.172711.8986
20.50090.25960.14191.22220.17790.7141-0.0158-0.0279-0.00720.1185-0.04280.2828-0.021-0.10070.05860.02580.02480.04850.08750.01790.1142-25.089378.454992.6981
30.3061-0.314-0.06561.34490.33660.8250.02740.0153-0.0075-0.10250.0007-0.0829-0.06650.029-0.02810.0205-0.0292-0.00620.08980.01110.0557-0.421953.367136.8191
40.562-0.2695-0.12731.16280.0780.6343-0.03170.0533-0.0299-0.1686-0.02820.19450.0921-0.09240.05990.0486-0.021-0.01910.09580.00770.0765-24.0007102.573560.0364
50.5970.3009-0.0720.9716-0.1820.6382-0.0125-0.05060.00570.1286-0.0348-0.15740.02320.07770.04740.0330.0278-0.02940.0869-0.01210.07389.06441.981944.4082
60.30680.32820.03111.81130.36760.6726-0.0238-0.0072-0.00560.02760.046-0.09110.09450.0326-0.02220.05850.0110.00320.09020.00320.04837.7429127.611719.4287
70.3346-0.36230.05461.6881-0.27680.87360.01330.01630.01320.02070.00920.12330.1385-0.0333-0.02250.0636-0.02140.01540.0892-0.0130.0904-20.692926.831784.5075
80.405-0.3603-0.01273.11310.02120.67870.0442-0.0290.01070.4365-0.0349-0.0471-0.02650.0231-0.00930.1717-0.0228-0.00950.09860.00920.09584.810353.568834.9219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 3255
2X-RAY DIFFRACTION2B4 - 3257
3X-RAY DIFFRACTION3C3 - 3258
4X-RAY DIFFRACTION4D5 - 3259
5X-RAY DIFFRACTION5E2 - 3260
6X-RAY DIFFRACTION6F10 - 3261
7X-RAY DIFFRACTION7G27 - 3262
8X-RAY DIFFRACTION8H9 - 3264

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