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- PDB-7fi3: Archaeal oligopeptide permease A (OppA) from Thermococcus kodakar... -

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Basic information

Entry
Database: PDB / ID: 7fi3
TitleArchaeal oligopeptide permease A (OppA) from Thermococcus kodakaraensis in complex with an endogenous pentapeptide
Components
  • ABC-type dipeptide/oligopeptide transport system
  • endogenous pentapeptide
KeywordsPEPTIDE BINDING PROTEIN / oligopeptide permease
Function / homologyCGP-CTERM domain / peptide transport / peptide transmembrane transporter activity / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / ABC-type dipeptide/oligopeptide transport system, probable periplasmic component
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsYokoyama, H. / Kamei, N. / Konishi, K. / Hara, K. / Hashimoto, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K07316 Japan
CitationJournal: Proteins / Year: 2022
Title: Structural basis for peptide recognition by archaeal oligopeptide permease A.
Authors: Yokoyama, H. / Kamei, N. / Konishi, K. / Hara, K. / Ishikawa, Y. / Matsui, I. / Forterre, P. / Hashimoto, H.
History
DepositionJul 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC-type dipeptide/oligopeptide transport system
B: ABC-type dipeptide/oligopeptide transport system
C: ABC-type dipeptide/oligopeptide transport system
D: ABC-type dipeptide/oligopeptide transport system
E: endogenous pentapeptide
F: endogenous pentapeptide
G: endogenous pentapeptide
H: endogenous pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,08825
Polymers339,6958
Non-polymers1,39317
Water23,4921304
1
A: ABC-type dipeptide/oligopeptide transport system
E: endogenous pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4367
Polymers84,9242
Non-polymers5125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-14 kcal/mol
Surface area26460 Å2
MethodPISA
2
B: ABC-type dipeptide/oligopeptide transport system
F: endogenous pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3446
Polymers84,9242
Non-polymers4204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-14 kcal/mol
Surface area26640 Å2
MethodPISA
3
C: ABC-type dipeptide/oligopeptide transport system
G: endogenous pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1546
Polymers84,9242
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-15 kcal/mol
Surface area26760 Å2
MethodPISA
4
D: ABC-type dipeptide/oligopeptide transport system
H: endogenous pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1546
Polymers84,9242
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-15 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.661, 118.635, 112.718
Angle α, β, γ (deg.)90.000, 105.320, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A34 - 757
211B34 - 757
122A34 - 757
222C34 - 757
133A34 - 757
233D34 - 757
144B34 - 757
244C34 - 757
155B34 - 757
255D34 - 757
166C34 - 757
266D34 - 757

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
ABC-type dipeptide/oligopeptide transport system


Mass: 84480.195 Da / Num. of mol.: 4 / Mutation: I302M, L446M, L557M, L636M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1804 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JJ92
#2: Protein/peptide
endogenous pentapeptide


Mass: 443.539 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 1321 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1304 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 1500, MIB (sodium malonate, imidazole, and boric acid)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 137907 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.139 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.694 / Num. unique obs: 20087 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 12.08 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 13814 10 %RANDOM
Rwork0.1586 ---
obs0.162 124069 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.42 Å2 / Biso mean: 26.299 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0.72 Å2
2--0.37 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23548 0 88 1304 24940
Biso mean--39.04 29.37 -
Num. residues----2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01324335
X-RAY DIFFRACTIONr_bond_other_d0.0010.01721168
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.64833153
X-RAY DIFFRACTIONr_angle_other_deg1.441.57849172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8152908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3623.4351316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.236153540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6641592
X-RAY DIFFRACTIONr_chiral_restr0.0840.23060
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0227484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025400
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A252940.07
12B252940.07
21A254160.06
22C254160.06
31A253790.06
32D253790.06
41B252800.06
42C252800.06
51B253310.07
52D253310.07
61C253210.07
62D253210.07
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 985 -
Rwork0.23 9084 -
all-10069 -
obs--100 %
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)
10.21710.0046-0.01550.15890.02350.37860.0128-0.0073-0.05670.0391-0.0168-0.0308-0.0114-0.02770.0040.04550.0002-0.01070.00710.01450.052632.6437-22.924728.1454
20.2243-0.0054-0.05580.29870.0630.3973-0.0470.0533-0.01330.01780.0270.02470.0338-0.15850.020.0147-0.0146-0.0030.1345-0.0250.02490.4605-6.8202-15.1945
30.3255-0.10560.09850.16840.07640.2477-0.03480.02040.0155-0.04120.0144-0.0001-0.10220.05620.02040.0806-0.0305-0.01980.0174-0.00260.037356.836113.607521.415
40.2355-0.0768-0.02520.4543-0.03240.2105-0.02990.06560.0164-0.01140.0265-0.062-0.0046-0.04230.00350.0569-0.0119-0.01390.04160.00970.021335.260616.1593-30.4957
522.7684-0.1646.95480.2222-1.358811.1485-0.3048-0.6170.0011-0.00030.0713-0.05390.1437-0.06230.23350.1080.0662-0.00860.2035-0.04980.107931.1763-20.000725.2543
64.91471.7477-2.11764.62152.52173.59330.09970.20510.0843-0.2268-0.29890.3095-0.2516-0.39940.19920.07770.004-0.00310.1215-0.03910.07514.4408-7.2915-13.233
76.77192.40620.44861.58330.25940.0436-0.3359-0.24760.2780.04230.3068-0.206300.0330.02910.29120.057-0.07050.2189-0.09870.236254.735311.865617.9862
80.9238-2.78292.54388.3993-7.68087.02440.07880.09720.0532-0.2252-0.2508-0.1840.20260.21970.1720.06310.0662-0.00110.133-0.0420.113534.908915.4059-26.2606
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 757
2X-RAY DIFFRACTION2B34 - 757
3X-RAY DIFFRACTION3C34 - 757
4X-RAY DIFFRACTION4D34 - 757
5X-RAY DIFFRACTION5E1 - 5
6X-RAY DIFFRACTION6F1 - 5
7X-RAY DIFFRACTION7G1 - 5
8X-RAY DIFFRACTION8H1 - 5

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