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- PDB-5d0y: Substrate bound S-component of folate ECF transporter -

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Basic information

Entry
Database: PDB / ID: 5d0y
TitleSubstrate bound S-component of folate ECF transporter
ComponentsConserved hypothetical membrane protein
KeywordsTRANSPORT PROTEIN / ECF transporter / folate / S-component / membrane protein / vitamin
Function / homology
Function and homology information


transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function
ECF transporter S component, folate family / ECF transporter, substrate-specific component / ECF transporter, substrate-specific component / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FOLIC ACID / : / Conserved hypothetical membrane protein
Similarity search - Component
Biological speciesLactobacillus delbrueckii subsp. bulgaricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.014 Å
AuthorsSwier, L.J.Y.M. / Guskov, A. / Slotboom, D.J.
Funding support1items
OrganizationGrant numberCountry
European Research Council282083
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
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Conserved hypothetical membrane protein
B: Conserved hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9224
Polymers41,0392
Non-polymers8832
Water0
1
A: Conserved hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9612
Polymers20,5201
Non-polymers4411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9612
Polymers20,5201
Non-polymers4411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.910, 77.540, 89.450
Angle α, β, γ (deg.)90.00, 116.36, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 13:167 )
211chain 'B' and (resseq 13:167 )

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Components

#1: Protein Conserved hypothetical membrane protein


Mass: 20519.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus (bacteria)
Gene: LBVIB27_08730, LBVIB44_08025 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A061BQC9, UniProt: Q1G930*PLUS
#2: Chemical ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N7O6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 71.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 24% 350 PEG MME, 100mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92017 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92017 Å / Relative weight: 1
ReflectionResolution: 3→60 Å / Num. obs: 21443 / % possible obs: 82.4 % / Redundancy: 2 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 4.3
Reflection shellResolution: 3→3.08 Å / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 2.18 / % possible all: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3M

5d3m


Resolution: 3.014→43.012 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 590 5.38 %Random selection
Rwork0.2348 ---
obs0.2376 10960 82.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 3.014→43.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 64 0 2456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112522
X-RAY DIFFRACTIONf_angle_d1.4293428
X-RAY DIFFRACTIONf_dihedral_angle_d18.513840
X-RAY DIFFRACTIONf_chiral_restr0.069398
X-RAY DIFFRACTIONf_plane_restr0.005400
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1196X-RAY DIFFRACTIONPOSITIONAL0.05
12B1196X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0145-3.31770.3385980.26741343X-RAY DIFFRACTION44
3.7976-4.78360.24971760.20523112X-RAY DIFFRACTION98.5
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)
11.6404-0.3859-0.57282.93740.96460.52360.0522-0.48510.1770.45630.1054-0.23620.16020.18670.00330.3735-0.1855-0.1410.66030.14620.45543.487617.655624.6586
20.72430.03750.22340.6058-0.15591.25440.3237-0.3153-0.00720.33950.117-0.1648-0.04040.20660.1510.3314-0.2069-0.07470.3285-0.00970.2862-7.075315.360416.7985
32.787-0.1455-1.54371.0908-0.09721.17130.2066-0.39050.0540.4558-0.36510.07040.0991-0.00380.09680.4015-0.2031-0.02850.3590.05190.1845-1.806125.037121.2557
40.1803-0.1756-0.2860.39910.11161.1396-0.0024-0.09260.0040.1501-0.05260.00530.01040.0738-0.06580.4109-0.19690.05810.3189-0.0460.1256-4.424727.70187.125
51.12710.9496-1.90942.4894-2.27983.50130.2543-0.2971-0.21640.34290.1159-0.0370.22270.15110.12450.3417-0.1633-0.05170.38120.04010.1896-11.300323.299822.7995
60.12350.121-0.51252.0281-1.31913.34720.04340.0029-0.04070.02440.04540.0070.0684-0.1231-0.02050.8317-0.5142-0.21840.81930.150.4056-12.255812.644936.0973
70.9235-0.32770.36820.40340.20240.5310.1586-0.5306-0.38470.46760.04870.06120.1383-0.1150.09090.4716-0.18660.05120.45970.09270.2329-19.503914.858925.3414
81.83351.7103-1.85253.0737-0.62513.26540.2087-0.1430.12090.103-0.11350.0585-0.0585-0.045-0.07120.2506-0.1017-0.00210.18820.13420.2596-16.987327.09349.4003
91.33840.5865-0.88953.7956-1.13411.6340.2225-0.321-0.2170.2593-0.3083-0.1970.1819-0.1278-0.19260.236-0.1698-0.07020.21390.08570.3133-17.026112.2316.16
101.10840.7481-0.01320.9153-0.07870.60860.0241-0.1760.31220.4089-0.28220.3776-0.0629-0.124-0.6680.2275-0.20450.21160.1448-0.02130.481-47.37583.062915.4127
110.7826-0.04220.03740.0646-0.03920.02220.3798-0.52990.41850.2982-0.2999-0.0583-0.2586-0.2789-0.10150.3899-0.16630.06870.3858-0.08990.1932-43.3999-1.497621.0162
121.08880.57031.31395.12461.44443.27720.1375-0.02260.03540.02130.0555-0.2471-0.19430.0985-0.00770.8119-0.23490.19980.7156-0.35910.6376-39.904412.787633.1945
132.07390.86181.08440.6766-0.04431.59380.0309-0.38190.33720.1395-0.04610.0042-0.0455-0.03210.0670.2655-0.15430.03780.4991-0.20930.2594-30.71867.387125.4624
141.54250.73170.19612.0718-0.3751.57420.1593-0.14340.0849-0.1787-0.1007-0.19210.00730.0526-0.00460.1775-0.0925-0.03140.22870.02720.2447-30.90581.457615.0107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 100 )
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 106 )
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 120 )
8X-RAY DIFFRACTION8chain 'A' and (resid 121 through 137 )
9X-RAY DIFFRACTION9chain 'A' and (resid 138 through 167 )
10X-RAY DIFFRACTION10chain 'B' and (resid 13 through 43 )
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 100 )
12X-RAY DIFFRACTION12chain 'B' and (resid 101 through 106 )
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 120 )
14X-RAY DIFFRACTION14chain 'B' and (resid 121 through 167 )

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