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- PDB-5jsz: Folate ECF transporter: apo state -

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Basic information

Entry
Database: PDB / ID: 5jsz
TitleFolate ECF transporter: apo state
Components
  • Conserved hypothetical membrane protein
  • Energy-coupling factor transporter ATP-binding protein EcfA1
  • Energy-coupling factor transporter ATP-binding protein EcfA2
  • Energy-coupling factor transporter transmembrane protein EcfT
KeywordsTRANSPORT PROTEIN / ECF transporter / folate / membrane protein / vitamin transport
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 / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ECF transporter S component, folate family / 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 / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Cobalt import ATP-binding protein cbiO. ...ECF transporter S component, folate family / 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 / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit / Arp2/3 complex 21 kDa subunit ARPC3 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Energy-coupling factor transporter transmembrane protein EcfT / Conserved hypothetical membrane protein / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1
Similarity search - Component
Biological speciesLactobacillus delbrueckii subsp. bulgaricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsSwier, L.J.Y.M. / Guskov, A. / Slotboom, D.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Research Council282083 Netherlands
CitationJournal: Nat Commun / Year: 2016
Title: Structural insight in the toppling mechanism of an energy-coupling factor transporter.
Authors: Swier, L.J. / Guskov, A. / Slotboom, D.J.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionMay 18, 2016ID: 5D7T
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)231,2258
Polymers231,2258
Non-polymers00
Water0
1
A: Energy-coupling factor transporter ATP-binding protein EcfA1
B: Energy-coupling factor transporter ATP-binding protein EcfA2
C: Conserved hypothetical membrane protein
D: Energy-coupling factor transporter transmembrane protein EcfT


Theoretical massNumber of molelcules
Total (without water)115,6124
Polymers115,6124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-94 kcal/mol
Surface area45090 Å2
MethodPISA
2
E: Energy-coupling factor transporter ATP-binding protein EcfA1
F: Energy-coupling factor transporter ATP-binding protein EcfA2
G: Conserved hypothetical membrane protein
H: Energy-coupling factor transporter transmembrane protein EcfT


Theoretical massNumber of molelcules
Total (without water)115,6124
Polymers115,6124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-100 kcal/mol
Surface area44740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.820, 95.320, 107.570
Angle α, β, γ (deg.)83.45, 65.75, 61.99
Int Tables number1
Space group name H-MP1

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Components

#1: 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
Details: 10 HIS-TAG AND TEV-CLEAVAGE SITE AT N-TERMINUS
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria)
Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778
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
#2: 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 subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria)
Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778
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
#3: Protein Conserved hypothetical membrane protein


Mass: 20483.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: STREPII TAG AT C-TERMINUS
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778) (bacteria)
Strain: ATCC 11842 / DSM 20081 / JCM 1002 / NBRC 13953 / NCIMB 11778
Gene: Ldb1625 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1G929
#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 subsp. bulgaricus (bacteria)
Gene: ecfT, AT236_00396, CFL1_00754, SB57_06620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A061BSU4

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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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50MM TRIS, 17% PEG 350MME, 2% NG, 10MM SPERMIDINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 52519 / % possible obs: 92.6 % / Redundancy: 1.76 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.54
Reflection shellResolution: 3→3.08 Å / Redundancy: 1.72 % / % possible all: 86.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3M

5d3m


Resolution: 3.004→49.004 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 35
RfactorNum. reflection% reflection
Rfree0.2774 2088 5.03 %
Rwork0.2328 --
obs0.235 41540 73.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.004→49.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15394 0 0 0 15394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515720
X-RAY DIFFRACTIONf_angle_d1.00621304
X-RAY DIFFRACTIONf_dihedral_angle_d17.8089366
X-RAY DIFFRACTIONf_chiral_restr0.0552464
X-RAY DIFFRACTIONf_plane_restr0.0062670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0042-3.0740.5054190.3849450X-RAY DIFFRACTION12
3.074-3.15090.493320.3363764X-RAY DIFFRACTION21
3.1509-3.23610.3642600.32641195X-RAY DIFFRACTION34
3.2361-3.33130.37351020.33381851X-RAY DIFFRACTION53
3.3313-3.43880.3711470.29812557X-RAY DIFFRACTION71
3.4388-3.56160.32471580.27163106X-RAY DIFFRACTION87
3.5616-3.70420.2911900.25183429X-RAY DIFFRACTION96
3.7042-3.87270.32191880.23413321X-RAY DIFFRACTION94
3.8727-4.07680.26841620.21253376X-RAY DIFFRACTION94
4.0768-4.33210.2541670.19673340X-RAY DIFFRACTION93
4.3321-4.66630.22251520.18843281X-RAY DIFFRACTION91
4.6663-5.13550.23481580.19383212X-RAY DIFFRACTION90
5.1355-5.87750.26561930.24293236X-RAY DIFFRACTION91
5.8775-7.4010.29721820.28853150X-RAY DIFFRACTION89
7.401-49.01090.26751780.22273184X-RAY DIFFRACTION89
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)
13.86031.48481.56372.09490.0893.2554-0.02630.3356-0.16070.17470.0334-0.30140.0660.2824-0.01460.28070.16560.01830.2852-0.0280.303718.438449.833-24.7274
25.1377-1.85070.54681.92271.06032.2511-0.1609-0.3723-0.20420.4664-0.2688-0.02270.32280.05770.29590.4633-0.0128-0.09640.4068-0.03810.39139.4563.30041.0511
32.55920.8478-1.25185.69432.72422.42180.58860.5382-0.63110.3056-0.04540.21890.94-1.2321-0.04830.6258-0.2444-0.40030.6621-0.05050.6831-23.627552.7384-27.7814
41.4734-1.02560.82141.64-0.57912.1306-0.09760.43290.1745-0.1782-0.3590.0302-0.0982-0.87690.37120.69530.083-0.07650.83980.02670.639-18.865871.3181-35.089
54.8551-1.8087-2.68761.63110.43563.4975-0.0649-0.22750.11610.1416-0.0934-0.102-0.06180.31340.14670.2983-0.1284-0.09010.4124-0.0060.289818.6555118.389324.1709
65.1971.3459-0.58882.63120.81361.70630.10730.53990.3058-0.1508-0.2824-0.2043-0.18470.20410.08610.4007-0.00020.08120.3791-0.03980.27659.5816104.9939-1.5604
73.3232-0.98840.00325.75184.01354.85240.3107-0.49270.4507-0.27340.03810.4495-1.4804-1.0352-0.43390.61790.09430.27250.73560.00460.6002-23.4077115.522927.2957
82.13181.4757-1.6012.6774-1.01062.3052-0.1288-0.4982-0.10270.5664-0.36980.34190.4148-0.5110.45980.7247-0.13180.15110.7285-0.08980.6353-18.809997.088634.5477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 282)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 280)
3X-RAY DIFFRACTION3(chain 'C' and resid 9 through 173)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 264)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 282)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 280)
7X-RAY DIFFRACTION7(chain 'G' and resid 9 through 173)
8X-RAY DIFFRACTION8(chain 'H' and resid 6 through 264)

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