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- PDB-5l22: PrtD T1SS ABC transporter -

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Basic information

Entry
Database: PDB / ID: 5l22
TitlePrtD T1SS ABC transporter
ComponentsABC transporter (HlyB subfamily)
KeywordsPROTEIN TRANSPORT / T1SS / ABC transporter / ATPase / secretion
Function / homology
Function and homology information


protein secretion by the type I secretion system / type I protein secretion system complex / plasma membrane => GO:0005886 / ATPase-coupled transmembrane transporter activity / ATP binding / metal ion binding
Similarity search - Function
ATPase, type I secretion system, PrtD-like / 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-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...ATPase, type I secretion system, PrtD-like / 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-like, conserved site / ABC transporters family signature. / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ABC transporter (HlyB subfamily)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 Å
AuthorsMorgan, J.L.W. / Zimmer, J.
CitationJournal: Structure / Year: 2017
Title: Structure of a Type-1 Secretion System ABC Transporter.
Authors: Morgan, J.L. / Acheson, J.F. / Zimmer, J.
History
DepositionJul 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ABC transporter (HlyB subfamily)
A: ABC transporter (HlyB subfamily)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3856
Polymers128,4822
Non-polymers9034
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15290 Å2
ΔGint-119 kcal/mol
Surface area43790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.672, 97.938, 179.823
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ABC transporter (HlyB subfamily)


Mass: 64241.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: abcT5, aq_1097 / Production host: Escherichia coli (E. coli) / References: UniProt: O67184
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 4.07 Å3/Da / Density % sol: 69.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 16-21% PEG 1000, 100-400 mM (NH4)2SO4, with 10 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0007 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 3.12→34.3 Å / Num. obs: 35413 / % possible obs: 97.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.3
Reflection shellResolution: 3.12→3.27 Å / Rmerge(I) obs: 0.809

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.15→33.536 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2758 1730 4.99 %
Rwork0.2234 --
obs0.226 34695 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→33.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8499 0 56 0 8555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038721
X-RAY DIFFRACTIONf_angle_d0.73611832
X-RAY DIFFRACTIONf_dihedral_angle_d13.0883228
X-RAY DIFFRACTIONf_chiral_restr0.0281402
X-RAY DIFFRACTIONf_plane_restr0.0031461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1501-3.24270.39861360.34312559X-RAY DIFFRACTION93
3.2427-3.34730.33121400.29932764X-RAY DIFFRACTION98
3.3473-3.46680.3611390.3162708X-RAY DIFFRACTION99
3.4668-3.60550.2981630.26882756X-RAY DIFFRACTION100
3.6055-3.76940.40161280.30792693X-RAY DIFFRACTION97
3.7694-3.96780.32771560.27012664X-RAY DIFFRACTION97
3.9678-4.21590.28891470.21462786X-RAY DIFFRACTION100
4.2159-4.54070.22081510.17632789X-RAY DIFFRACTION100
4.5407-4.99630.24071290.17122795X-RAY DIFFRACTION100
4.9963-5.71620.2431520.19612783X-RAY DIFFRACTION100
5.7162-7.19020.28671530.24072813X-RAY DIFFRACTION100
7.1902-33.53760.23121360.19452855X-RAY DIFFRACTION99
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)
16.90531.5231-0.00933.8919-0.83775.389-0.67580.48610.14572.4383-0.39311.6013-0.5634-1.35620.47712.05960.00570.55441.1903-0.40610.80714.39219.419566.3033
22.5864-0.5824-3.21391.31461.1534.8875-0.0802-0.76380.11280.70640.00880.36710.3458-0.16050.09731.01380.03760.12290.92260.00040.912210.7425.368749.3338
32.6088-0.0208-0.4181.4843-0.22131.19720.0674-0.63390.51050.51690.00750.0138-0.25370.1371-0.14370.841-0.0195-0.0720.4483-0.12271.026539.252212.427524.5379
45.4604-1.6848-3.21793.68990.15757.51040.2455-1.18850.55741.7516-0.34011.6348-0.1686-0.925-0.05551.3134-0.32620.51021.4593-0.34491.4187-15.7999-0.102850.6941
55.04250.4192-5.40541.3590.39278.7288-0.42450.0343-0.03310.7341-0.31930.26620.8464-1.58110.66061.226-0.20390.35251.1148-0.18431.264-3.75380.606941.555
68.1982.64480.38936.786-3.07591.7388-1.11570.54841.09650.6111-0.055-0.4241-0.3959-1.61580.94730.9550.34970.23321.4276-0.15941.7326-13.425221.653248.303
76.0378-2.0295-5.71841.4930.15086.99610.2915-0.27960.89030.72560.15040.1371-0.5118-0.8649-0.47671.1109-0.02860.21480.9805-0.3811.292511.289619.664640.1283
87.7405-3.7012-7.02433.05352.63696.35110.2996-1.20770.82230.2451-0.02310.39180.1587-0.3868-0.25611.113-0.00070.36451.5759-0.32021.5648-8.112512.060147.1692
94.70470.2719-2.55515.1152-0.33376.44160.09940.24380.4174-0.27660.1230.7311-0.3732-0.8455-0.18710.61580.0086-0.22730.35010.07740.978618.01463.9668-2.1451
103.75061.28750.56155.2146-0.19244.32380.403-0.4387-0.63840.3722-0.29180.45490.5328-0.1705-0.11410.8857-0.00990.0520.2670.02781.116629.035-9.507510.7009
114.0811-1.28631.30633.8446-1.27314.50550.24230.5985-0.5514-0.8227-0.3554-0.1720.56330.490.19550.793-0.0545-0.07880.31970.05710.951334.2038-1.5306-7.7234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 10 through 57 )
2X-RAY DIFFRACTION2chain 'B' and (resid 58 through 262 )
3X-RAY DIFFRACTION3chain 'B' and (resid 263 through 559 )
4X-RAY DIFFRACTION4chain 'A' and (resid 11 through 55 )
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 179 )
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 265 )
8X-RAY DIFFRACTION8chain 'A' and (resid 266 through 312 )
9X-RAY DIFFRACTION9chain 'A' and (resid 313 through 392 )
10X-RAY DIFFRACTION10chain 'A' and (resid 393 through 500 )
11X-RAY DIFFRACTION11chain 'A' and (resid 501 through 559 )

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