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- PDB-4s0f: Crystal structure of the peptidase-containing ABC transporter PCA... -

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Basic information

Entry
Database: PDB / ID: 4s0f
TitleCrystal structure of the peptidase-containing ABC transporter PCAT1 E648Q mutant complexed with ATPgS in an occluded conformation
ComponentsABC-type bacteriocin transporter
KeywordsTRANSPORT PROTEIN/HYDROLASE / C39 peptidase / ABC transporter / bacteriocin transporter / bi-functional ABC transporter / ATP-binding cassette transporters / Membrane / TRANSPORT PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


ABC-type bacteriocin transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / membrane
Similarity search - Function
Peptidase C39, ABC-type bacteriocin transporter / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / 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 ...Peptidase C39, ABC-type bacteriocin transporter / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ABC-type bacteriocin transporter
Similarity search - Component
Biological speciesRuminiclostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.515 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 30, 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,4064
Polymers162,3602
Non-polymers1,0462
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)230.000, 230.000, 89.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein ABC-type bacteriocin transporter


Mass: 81179.812 Da / Num. of mol.: 2 / Mutation: E648Q
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
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 7% PEG1500, 20mM CaCl2, 100 mM sodium citrate, pH 5.2-5.6, 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: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 5.5→50 Å / Num. all: 8276 / Num. obs: 8210 / % possible obs: 99.2 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
5.5-5.7199.2
5.7-5.92195.6
5.92-6.19198.3
6.19-6.52199.9
6.52-6.931100
6.93-7.461100
7.46-8.211100
8.21-9.391100
9.39-11.81100
11.8-50198.6

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RY2, 3VX4

4ry2

3vx4


Resolution: 5.515→19.983 Å / SU ML: 1.04 / σ(F): 2 / Phase error: 43.36 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3139 306 4.76 %Random
Rwork0.3005 ---
obs0.3013 6433 80.89 %-
all-7953 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.515→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 62 0 5636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035638
X-RAY DIFFRACTIONf_angle_d0.6887856
X-RAY DIFFRACTIONf_dihedral_angle_d5.7161146
X-RAY DIFFRACTIONf_chiral_restr0.0231066
X-RAY DIFFRACTIONf_plane_restr0.0031130
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection obs% reflection obs (%)
5.515-6.481690.4441475X-RAY DIFFRACTION147550.54
6.481-7.15520.40671203X-RAY DIFFRACTION120399.92
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)
10.1404-0.2533-0.18320.9246-0.54041.8138-0.6115-0.2125-0.13240.059-0.7584-1.15030.5867-0.251-3.05012.4565-0.08171.36461.01530.6980.507541.1955-37.290938.031
24.31190.14240.47750.3605-0.33970.3353-0.99640.47092.04720.00870.316-0.7479-0.6263-0.7024-0.92080.9701-1.3236-0.52370.7115-0.09541.443566.7548-20.387428.7076
3-0.00750.03070.0280.09620.0050.0909-0.06920.0223-0.3052-0.24440.3280.2841-0.161-0.03420.60911.6529-1.1564-0.94570.76860.28610.112747.0204-48.59220.322
40.0174-0.0172-0.20190.06550.12250.191-0.15830.36661.2993-0.37020.21840.3262-0.85540.38820.07292.7561-1.1415-0.95331.38911.17312.518564.913-10.093411.1503
51.4349-0.13570.00580.0147-0.0083-0.03130.4389-0.38070.543-0.14220.477-0.02180.9825-1.08941.35710.905-1.70730.58291.87720.140.567539.3937-44.150617.8079
60.00670.0019-0.00790.2859-0.0080.02540.0290.1580.2232-0.3134-0.0763-0.2864-0.71860.79860.0831.3244-1.50530.07341.5915-0.1031.672864.0932-25.842621.5603
70.2293-0.0262-0.05580.1414-0.06520.3459-0.67570.7226-0.3043-0.76560.7597-0.8105-0.02450.7776-0.9703-0.8121-2.7387-1.2212-0.9516-0.72082.171999.3834-1.873228.3167
80.58770.37730.05450.2346-0.17710.5160.60460.95430.6397-0.27020.96590.1517-0.01740.37923.65351.2884-3.2492-1.16190.6081-0.67221.987485.287513.124338.9112
90.2109-0.1062-0.26240.3183-0.17770.4461-0.27550.45250.8226-0.33360.2609-0.3122-0.30650.3285-0.71342.7807-2.19220.52221.22050.36533.3725107.867913.393223.8554
102.4144-0.29140.47791.02530.55984.59760.06380.16330.2038-0.22870.4478-0.2574-1.08631.21851.73061.5492-0.9312-0.7721.03740.16991.456335.8544-17.6944.3638
112.0224-0.00530.10120.5297-0.31940.2994-0.66630.98621.5258-0.2787-0.5362-0.5559-0.61050.6299-2.2650.9944-1.2673-0.13741.29610.40871.084635.499-34.79078.1057
120.2981-0.2313-0.25380.1790.17680.4237-0.2230.1126-0.83150.4008-0.0024-0.50150.6248-0.62750.11233.5472-0.18820.50630.90650.6754.006360.54442.810418.7846
130.13890.2720.33750.55730.089-0.0175-0.47750.55080.15640.0468-0.0942-0.488-0.70420.3923-0.39891.4273-1.1694-1.25471.18650.41861.326949.97-12.730528.5811
141.35681.4750.07071.6542-0.04550.5626-0.75940.92940.7483-0.62090.2702-1.03570.4912-1.2305-0.68951.6514-1.4357-0.23330.29230.021.438332.3287-26.441726.1957
150.72560.853-1.21791.4136-1.62642.51180.34660.72551.1324-0.1777-0.63820.34750.4551-1.1967-1.02394.0641-2.3206-0.32960.59371.11653.648367.333726.673917.8543
160.6810.0524-0.15040.1704-0.17680.241-0.4120.48480.2022-0.07380.46670.3701-0.14620.167-0.62912.3122-3.8189-0.27823.10852.0863.217176.188413.1176.656
170.04250.14580.02940.58720.05830.01730.13690.17720.70680.0146-0.0406-0.3498-0.06540.21920.40112.0993-3.0101-0.58871.95140.72111.915887.07888.77437.0066
180.3337-0.21480.55360.131-0.38561.0825-0.9518-0.06031.6758-0.4522-1.5853-1.1825-0.22251.8485-0.64534.2023-1.38920.50323.11371.36385.574588.523830.075818.6938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 158:233)
2X-RAY DIFFRACTION2(chain A and resid 234:298)
3X-RAY DIFFRACTION3(chain A and resid 299:320)
4X-RAY DIFFRACTION4(chain A and resid 321:389)
5X-RAY DIFFRACTION5(chain A and resid 390:439)
6X-RAY DIFFRACTION6(chain A and resid 440:463)
7X-RAY DIFFRACTION7(chain A and resid 485:573)
8X-RAY DIFFRACTION8(chain A and resid 574:671)
9X-RAY DIFFRACTION9(chain A and resid 672:722)
10X-RAY DIFFRACTION10(chain B and resid 158:186)
11X-RAY DIFFRACTION11(chain B and resid 187:239)
12X-RAY DIFFRACTION12(chain B and resid 240:275)
13X-RAY DIFFRACTION13(chain B and resid 276:388)
14X-RAY DIFFRACTION14(chain B and resid 389:457)
15X-RAY DIFFRACTION15(chain B and resid 458:551)
16X-RAY DIFFRACTION16(chain B and resid 552:591)
17X-RAY DIFFRACTION17(chain B and resid 592:643)
18X-RAY DIFFRACTION18(chain B and resid 644:722)

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