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- PDB-6fnp: Crystal structure of ECF-CbrT, a cobalamin transporter -

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Basic information

Entry
Database: PDB / ID: 6fnp
TitleCrystal structure of ECF-CbrT, a cobalamin transporter
Components
  • Energy-coupling factor transporter ATP-binding protein EcfA1
  • Energy-coupling factor transporter ATP-binding protein EcfA2
  • Energy-coupling factor transporter transmembrane protein EcfT
  • Membrane protein
KeywordsTRANSPORT PROTEIN / Vitamin B12 / ECF transporter / Membrane Protein / Cobalamin / ABC transporter
Function / homology
Function and homology information


Translocases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / : / Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit ...ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / : / Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ECF transporter S component / Energy-coupling factor transporter transmembrane protein EcfT / Conserved hypothetical membrane protein / Energy-coupling factor transporter transmembrane protein EcfT / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1
Similarity search - Component
Biological speciesLactobacillus delbrueckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSantos, J.A. / Rempel, S. / Guskov, A. / Slotboom, D.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWO865.11.001 Netherlands
CitationJournal: Elife / Year: 2018
Title: Functional and structural characterization of an ECF-type ABC transporter for vitamin B12.
Authors: Santos, J.A. / Rempel, S. / Mous, S.T. / Pereira, C.T. / Ter Beek, J. / de Gier, J.W. / Guskov, A. / Slotboom, D.J.
History
DepositionFeb 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane protein
B: Energy-coupling factor transporter ATP-binding protein EcfA1
C: Energy-coupling factor transporter ATP-binding protein EcfA2
D: Energy-coupling factor transporter transmembrane protein EcfT
E: Membrane protein
F: Energy-coupling factor transporter ATP-binding protein EcfA1
G: Energy-coupling factor transporter ATP-binding protein EcfA2
H: Energy-coupling factor transporter transmembrane protein EcfT


Theoretical massNumber of molelcules
Total (without water)231,0158
Polymers231,0158
Non-polymers00
Water00
1
A: Membrane protein
B: Energy-coupling factor transporter ATP-binding protein EcfA1
C: Energy-coupling factor transporter ATP-binding protein EcfA2
D: Energy-coupling factor transporter transmembrane protein EcfT


Theoretical massNumber of molelcules
Total (without water)115,5074
Polymers115,5074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-89 kcal/mol
Surface area44430 Å2
MethodPISA
2
E: Membrane protein
F: Energy-coupling factor transporter ATP-binding protein EcfA1
G: Energy-coupling factor transporter ATP-binding protein EcfA2
H: Energy-coupling factor transporter transmembrane protein EcfT


Theoretical massNumber of molelcules
Total (without water)115,5074
Polymers115,5074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-72 kcal/mol
Surface area49120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.470, 92.860, 105.510
Angle α, β, γ (deg.)72.57, 66.27, 62.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Membrane protein / Predicted membrane protein / Substrate-specific component CbrT of predicted cobalamin ECF transporter


Mass: 20378.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: AT236_00087, CFL1_01875, LBUL87_0070, SB57_03475 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A061BRW7, UniProt: Q1G7W0*PLUS
#2: Protein Energy-coupling factor transporter ATP-binding protein EcfA1 / ECF transporter A component EcfA1


Mass: 33166.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: ecfA1, cbiO1, Ldb0424 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1GBJ0, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#3: Protein Energy-coupling factor transporter ATP-binding protein EcfA2 / ECF transporter A component EcfA2


Mass: 31672.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: ecfA2, cbiO2, Ldb0425 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1GBI9, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#4: Protein Energy-coupling factor transporter transmembrane protein EcfT / ECF transporter T component EcfT


Mass: 30290.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: ecfT, AT236_00396, CFL1_00754, SB57_06620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A061BSU4, UniProt: Q1GBI8*PLUS

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium chloride 0.1 M Sodium citrate 5.5 37% (v/v) Pentaerythritol propoxylate 5/4 PO/OH, 10% ANAPOE C12E10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999815963 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999815963 Å / Relative weight: 1
ReflectionResolution: 3.4→47.802 Å / Num. obs: 31753 / % possible obs: 88.29 % / Redundancy: 2 % / Net I/σ(I): 0.98
Reflection shellResolution: 3.4→3.4 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jsz

5jsz


Resolution: 3.4→47.802 Å / Cross valid method: FREE R-VALUE / σ(F): 2.57 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2934 1754 5.52 %
Rwork0.2376 --
obs0.2458 31753 88.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→47.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15083 0 0 0 15083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115403
X-RAY DIFFRACTIONf_angle_d1.48720887
X-RAY DIFFRACTIONf_dihedral_angle_d6.2719164
X-RAY DIFFRACTIONf_chiral_restr0.0662420
X-RAY DIFFRACTIONf_plane_restr0.0092623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4003-3.510.30111380.20122651X-RAY DIFFRACTION82
3.51-3.63540.23881500.17612829X-RAY DIFFRACTION86
3.6354-3.78090.25531450.18292758X-RAY DIFFRACTION85
3.7809-3.95290.29761360.19192593X-RAY DIFFRACTION80
3.9529-4.16120.25731550.1922939X-RAY DIFFRACTION89
4.1612-4.42170.28571530.20652914X-RAY DIFFRACTION88
4.4217-4.76280.29231470.23372778X-RAY DIFFRACTION86
4.7628-5.24150.2991460.25842779X-RAY DIFFRACTION85
5.2415-5.99870.3741370.32442607X-RAY DIFFRACTION80
5.9987-7.55270.33481500.35262850X-RAY DIFFRACTION87
7.5527-47.26970.33421300.352461X-RAY DIFFRACTION75
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)
1-0.0397-0.00710.0155-0.0330.0059-0.0288-0.0145-0.0922-0.02810.043-0.0452-0.0117-0.00570.0403-0.2768-0.680.10390.0382-0.9015-0.3613-0.470555.0419-27.212528.8529
2-0.08070.02040.0135-0.09850.0901-0.15440.02290.0725-0.0202-0.01590.04280.04010.0435-0.09280.2327-1.5839-0.0911-0.0393-1.8131-0.7349-1.004225.3532-17.2649-1.5009
3-0.1092-0.05080.0543-0.09910.0274-0.15130.0053-0.0616-0.00810.05710.0440.0303-0.0336-0.09970.2497-1.765-0.0237-0.0639-1.8561-0.6067-0.979114.1384-29.556823.4638
4-0.13930.05660.0548-0.1210.0622-0.1512-0.1288-0.24660.01270.237-0.031-0.1197-0.12340.2196-0.4922-1.18640.01120.0451-1.3831-0.6604-0.82453.5461-9.424234.7044
50.0102-0.0046-0.00130.0038-0.01880.0224-0.0204-0.01410.00330.0120.0017-0.0163-0.02760.0165-0.0402-0.20830.002-0.0481-0.2028-0.025-0.172356.4078-36.903164.7518
6-0.0448-0.0171-0.0011-0.05830.0398-0.0754-0.00480.00070.0568-0.00320.00310.0597-0.055-0.1151-0.0567-0.70320.1124-0.0599-0.8761-0.275-0.589525.0328-45.701397.2612
7-0.03790.0269-0.0227-0.02250.0105-0.043-0.036-0.01180.02060.0425-0.0090.0145-0.02620.0036-0.2106-0.4568-0.0360.0551-0.5229-0.1272-0.378314.192-33.609872.018
8-0.0487-0.0188-0.03390.01-0.0363-0.0029-0.04950.0692-0.0389-0.1024-0.0495-0.07240.090.0856-0.2497-0.45620.07590.0132-0.54-0.1637-0.356154.4512-53.474261.7841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 175)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 280)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 282)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 264)
5X-RAY DIFFRACTION5(chain 'E' and resid 8 through 157)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 280)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 282)
8X-RAY DIFFRACTION8(chain 'H' and resid 6 through 264)

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