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- PDB-4ry2: Crystal structure of the peptidase-containing ABC transporter PCAT1 -

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Basic information

Entry
Database: PDB / ID: 4ry2
TitleCrystal structure of the peptidase-containing ABC transporter PCAT1
ComponentsABC-type bacteriocin transporter
KeywordsTRANSPORT PROTEIN/HYDROLASE / C39 peptidase / ABC transporter / bacteriocin transporter / bi-functional ABC transporter / ATP-binding cassette transporters / ATP Binding / Membrane / TRANSPORT PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


ABC-type bacteriocin transporter activity / ABC-type oligopeptide transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Peptidase C39, ABC-type bacteriocin transporter / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Cysteine proteinases / Cathepsin B; Chain A / Type 1 protein exporter / ABC transporter transmembrane region ...Peptidase C39, ABC-type bacteriocin transporter / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Cysteine proteinases / Cathepsin B; Chain A / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Alpha-Beta Complex / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ABC-type bacteriocin transporter
Similarity search - Component
Biological speciesRuminiclostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.611 Å
AuthorsLin, D.L. / Huang, S. / Chen, J.
CitationJournal: Nature / Year: 2015
Title: Crystal structures of a polypeptide processing and secretion transporter.
Authors: Lin, D.Y. / Huang, S. / Chen, J.
History
DepositionDec 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: ABC-type bacteriocin transporter
B: ABC-type bacteriocin transporter


Theoretical massNumber of molelcules
Total (without water)162,3622
Polymers162,3622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-104 kcal/mol
Surface area66730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.590, 89.730, 296.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC-type bacteriocin transporter


Mass: 81180.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum ATCC 27405 (bacteria)
Strain: ATCC 27405 / Gene: ABN51770.1, Cthe_0534 / Plasmid: pMCSG20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: A3DCU1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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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: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 19-22% PEG400, 100 mM sodium citrate, pH 5.2-5.4, and 1.4 mM N,N-bis-(3-D-Gluconamidopropyl). , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2013
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 3.61→50 Å / Num. obs: 20843 / % possible obs: 94 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.61-3.74190.7
3.74-3.89191.8
3.89-4.07191.9
4.07-4.28193
4.28-4.55196
4.55-4.9198.4
4.9-5.39199.7
5.39-6.171100
6.17-7.771100
7.77-50198.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QF4

3qf4


Resolution: 3.611→19.966 Å / SU ML: 0.59 / σ(F): 1.36 / Phase error: 37.05 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2894 1064 5.14 %Random
Rwork0.2658 ---
obs0.267 20686 75.23 %-
all-27497 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.611→19.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9927 0 0 0 9927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410076
X-RAY DIFFRACTIONf_angle_d0.7913706
X-RAY DIFFRACTIONf_dihedral_angle_d12.7013375
X-RAY DIFFRACTIONf_chiral_restr0.0291681
X-RAY DIFFRACTIONf_plane_restr0.0031746
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.6112-3.77450.3425210.343434334311
3.7745-3.9720.3883750.32981291129141
3.972-4.21870.35291070.33462042204264
4.2187-4.54090.33291450.29842778277886
4.5409-4.99140.34671850.27523190319098
4.9914-5.69890.32051910.312532353235100
5.6989-7.12530.38841650.354933043304100
7.1253-19.9660.20991750.200134393439100
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)
10.99921.446-0.21966.52643.76313.0489-0.30950.1265-0.20410.9520.74930.7370.749-1.5176-0.31261.4431-0.3159-0.26362.31210.61171.4016-14.7601-15.3072-23.5883
24.84020.1438-2.30671.8449-2.66045.3346-0.6128-0.09380.35330.28830.34010.0846-0.0099-0.28240.18391.53310.2144-0.39770.52040.0180.9908-4.243613.9774-69.4443
33.4261-1.1903-0.26991.95951.42310.84640.2426-1.01960.7366-0.3408-0.4660.27812.90120.5945-0.10491.82640.1948-0.36490.81960.33080.9046-3.95947.986-37.234
42.26590.43673.33330.38710.07363.24920.1206-1.1035-0.00030.1694-0.3202-0.23280.2833-0.68720.33251.06880.0187-0.47521.56910.0461.22441.7596-12.4166-46.3224
52.2223-2.6377-0.47796.444-0.41532.6488-0.5046-1.27340.1541-1.41710.4355-0.1805-0.894-1.77770.03391.0318-0.0735-0.44980.81220.02011.1507-9.616-6.3115-74.5755
60.65870.6084-0.69651.1161-0.54520.704-0.2076-1.1994-0.4821-0.41370.55680.76821.5718-1.4377-0.09852.5293-0.3663-0.79952.33650.54250.3632-9.99861.7767-39.805
74.6475-0.29410.20314.661-1.94314.7556-1.3964-0.8328-0.30991.66141.67021.7168-1.3069-1.96730.01151.61260.66010.10882.2579-0.13291.235-3.37787.63870.1993
85.6884-2.4218-1.70992.743-1.6023.48530.1457-1.88011.96093.63-0.0294-1.61530.37431.0410.03922.321-0.4541-0.58621.8816-0.28921.336915.182418.7913-11.2844
91.4338-0.5812-1.25788.57752.68585.79920.6463-2.57710.54973.5471.1842-1.72191.05842.8208-1.53151.42830.0429-0.03962.5994-0.41380.929323.999514.565-13.7589
108.5371-2.1289-0.18149.6586-2.42134.2241-1.69210.05741.51810.9975-0.43960.2982-2.19-0.74681.9392.92010.3616-0.6511.2882-0.32370.80138.273717.6009-0.5274
110.9357-0.10770.49020.0943-0.05740.25620.61180.175-0.0673-0.14350.4397-1.2771-0.41120.7575-0.3671.95211.0726-0.99522.2954-1.94292.661919.26894.022-2.0542
127.23587.0432-7.91956.8586-7.70728.6450.827-0.316-3.48930.433-1.8176-2.4658-0.37394.10651.27241.690.6909-0.77443.0091-0.87752.282322.505113.68273.9134
137.5646-1.04841.0037.33760.7939.383-2.1132-1.4419-0.17431.68582.8485-1.88481.2561.8028-0.79031.49750.4074-0.10922.0563-0.29931.140311.55636.77419.4581
141.9998-1.0229-0.88274.7784-4.45164.48840.1442-2.81790.8938-0.57160.4370.97060.2049-0.8236-0.25741.58651.0055-0.2463.20350.11231.1131-0.3538-2.065810.224
153.74390.974-0.70571.993-5.0232.4575-0.5412-0.7431-0.24172.0104-1.2647-0.5017-2.74080.73420.33772.47331.5925-0.59514.2048-0.31761.329310.3758-4.111818.2388
164.6774-0.94270.4492.86572.17274.0912-0.2096-0.99470.8066-0.79170.1099-0.8037-1.07250.86060.20391.7028-0.5876-0.20821.947-0.06271.821639.526711.1755-38.6515
173.50961.6583-0.21195.9227-1.79055.3737-0.8657-1.09840.7933-1.6456-1.1561-1.361-1.7985-0.38382.34641.14310.4962-0.24211.311-0.21041.433319.6119-18.6571-61.726
187.0569-0.2569-1.84463.79031.35342.8399-0.91990.68120.8665-0.8393-0.04070.21340.9522-0.20540.68321.2759-0.002-0.37670.4521-0.18231.0656-0.4595-16.3237-77.2153
191.7831-1.0534-0.40241.5097-0.72131.6597-0.1566-0.46440.27290.1298-0.1334-0.6323-1.07271.36480.32261.2665-0.4544-0.25890.91160.00851.026921.2881-9.3675-53.1675
201.04031.0953-2.19830.8045-2.38779.35810.149-0.47790.25330.103-0.45770.6046-2.81980.35550.58681.27130.1212-0.17490.8697-0.06931.366112.617910.8889-39.638
212.5189-1.53091.34546.69230.17840.7317-0.1718-0.559-0.2228-0.14840.0368-0.71510.34321.01350.1721.10260.0272-0.22911.08020.22160.87911.6083.021-69.8635
228.70827.5517-1.26396.6358-0.71572.2088-1.67852.1369-0.9518-0.4705-0.0837-2.1673-0.64620.997-1.08390.6461-0.1791-0.21063.6654-0.51111.400535.3873-12.7577-35.2455
232.18351.8757-1.18825.3332-0.37290.6936-1.4186-0.72120.7696-0.65711.2263-0.42690.4349-0.09110.15451.27490.0994-0.63443.62210.36721.315140.8314-10.3913-10.5402
241.9774-1.12042.48372.0493-1.04367.96350.49672.0762-2.21750.69980.0562-0.05720.60260.2465-0.53751.4598-0.18080.16612.59331.02411.43523.0286-22.9811-15.5793
254.70381.55071.70286.5112.35531.1416-0.5715-0.86030.47191.2215-0.52641.6015-0.36141.35840.54091.87280.0839-0.01062.59870.6270.992113.1317-21.44-8.8659
262.2984-1.29482.28313.8872-0.0235.7109-0.8959-0.23120.51151.72550.8940.4072-0.4265-1.3747-2.04082.1763-0.0107-0.24792.79841.60521.552822.2553-10.124-2.8257
271.6116-1.6391.28251.9472-1.63624.2296-0.4429-0.140.2116-0.4354-1.08660.2781.06570.19791.08551.7364-0.57891.03273.4264-0.40252.786516.3532-13.81753.4609
280.78690.6534-0.6930.4878-0.56940.78560.2285-0.2604-0.32060.4679-0.488-0.64840.1685-0.071-0.57951.6312-0.0319-0.39763.41421.53021.468727.5062-18.07251.6979
290.4580.1076-0.05260.93390.96392.1625-0.69970.18550.20460.2875-0.1812-0.41730.60110.00390.12043.5810.07580.0634.65060.91470.92529.3145-8.46467.7306
300.53070.65590.14571.44630.4580.17470.9127-2.1391-0.2911-0.7251-0.6331.1484-0.0953-1.97090.21562.03140.4013-0.73734.13140.25061.745938.4253-3.19287.1502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 12:155)
2X-RAY DIFFRACTION2(chain A and resid 156:232)
3X-RAY DIFFRACTION3(chain A and resid 233:296)
4X-RAY DIFFRACTION4(chain A and resid 297:389)
5X-RAY DIFFRACTION5(chain A and resid 390:439)
6X-RAY DIFFRACTION6(chain A and resid 440:467)
7X-RAY DIFFRACTION7(chain A and resid 468:555)
8X-RAY DIFFRACTION8(chain A and resid 556:601)
9X-RAY DIFFRACTION9(chain A and resid 602:639)
10X-RAY DIFFRACTION10(chain A and resid 640:646)
11X-RAY DIFFRACTION11(chain A and resid 647:653)
12X-RAY DIFFRACTION12(chain A and resid 654:670)
13X-RAY DIFFRACTION13(chain A and resid 671:692)
14X-RAY DIFFRACTION14(chain A and resid 693:700)
15X-RAY DIFFRACTION15(chain A and resid 701:724)
16X-RAY DIFFRACTION16(chain B and resid 12:152)
17X-RAY DIFFRACTION17(chain B and resid 153:186)
18X-RAY DIFFRACTION18(chain B and resid 187:235)
19X-RAY DIFFRACTION19(chain B and resid 236:313)
20X-RAY DIFFRACTION20(chain B and resid 314:378)
21X-RAY DIFFRACTION21(chain B and resid 379:457)
22X-RAY DIFFRACTION22(chain B and resid 458:471)
23X-RAY DIFFRACTION23(chain B and resid 484:551)
24X-RAY DIFFRACTION24(chain B and resid 552:592)
25X-RAY DIFFRACTION25(chain B and resid 593:643)
26X-RAY DIFFRACTION26(chain B and resid 644:655)
27X-RAY DIFFRACTION27(chain B and resid 656:661)
28X-RAY DIFFRACTION28(chain B and resid 662:680)
29X-RAY DIFFRACTION29(chain B and resid 681:686)
30X-RAY DIFFRACTION30(chain B and resid 687:722)

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