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- PDB-6fxg: Crystal structure of substrate binding domain 1 (SBD1) OF ABC tra... -

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Basic information

Entry
Database: PDB / ID: 6fxg
TitleCrystal structure of substrate binding domain 1 (SBD1) OF ABC transporter GLNPQ in complex with Asparagine
ComponentsAmino acid ABC transporter membrane protein PAAT family
KeywordsTRANSPORT PROTEIN / ASPARAGINE BINDING PROTEIN / AMINO ACID TRANSPORT / EXTRACELLULAR
Function / homology
Function and homology information


nitrogen compound transport / peptide transport / ATP-binding cassette (ABC) transporter complex / ligand-gated ion channel activity / protein transport
Similarity search - Function
Amino acid ABC transporter, permease protein, 3-TM domain / Bacterial extracellular solute-binding proteins, family 3 signature. / Solute-binding protein family 3, conserved site / ABC transporter type 1, transmembrane domain MetI-like / ABC transporter integral membrane type-1 domain profile. / Binding-protein-dependent transport system inner membrane component / MetI-like superfamily / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF ...Amino acid ABC transporter, permease protein, 3-TM domain / Bacterial extracellular solute-binding proteins, family 3 signature. / Solute-binding protein family 3, conserved site / ABC transporter type 1, transmembrane domain MetI-like / ABC transporter integral membrane type-1 domain profile. / Binding-protein-dependent transport system inner membrane component / MetI-like superfamily / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Ionotropic glutamate receptor / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARAGINE / ABC transporter permease subunit / Glutamine ABC transporter permease and substrate binding protein protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGuskov, A. / Schuurman-Wolters, G.K. / Poolman, B.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
ERCABCvolume, #670578 Netherlands
CitationJournal: To Be Published
Title: Crystal structure of substrate binding domain 1 (SBD1) OF ABC transporter GLNPQ in complex with Asparagine
Authors: Schuurman-Wolters, G.K. / Guskov, A. / Poolman, B.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid ABC transporter membrane protein PAAT family
B: Amino acid ABC transporter membrane protein PAAT family
C: Amino acid ABC transporter membrane protein PAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5206
Polymers74,1243
Non-polymers3963
Water16,952941
1
A: Amino acid ABC transporter membrane protein PAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8402
Polymers24,7081
Non-polymers1321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amino acid ABC transporter membrane protein PAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8402
Polymers24,7081
Non-polymers1321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amino acid ABC transporter membrane protein PAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8402
Polymers24,7081
Non-polymers1321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.870, 74.270, 110.240
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amino acid ABC transporter membrane protein PAAT family


Mass: 24707.889 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GM are cloning artefacts, the real sequence starts from E, which should be # 27
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: LL275_1813 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A1V0NHP2, UniProt: Q9CES5*PLUS
#2: Chemical ChemComp-ASN / ASPARAGINE / Asparagine


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 941 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 273 K / Method: microbatch / pH: 4.5
Details: 0.1M CH3COONa pH4.5, 0.05 M (CH3COO)Ca2, 40 % v/v propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→44.261 Å / Num. obs: 135138 / % possible obs: 92.5 % / Redundancy: 1.84 % / Rrim(I) all: 0.04 / Net I/σ(I): 15.2
Reflection shellResolution: 1.7→1.72 Å / Rrim(I) all: 0.101 / % possible all: 74

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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: 4KPT
Resolution: 1.7→44.26 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 16.99
RfactorNum. reflection% reflection
Rfree0.17 6742 4.99 %
Rwork0.136 --
obs0.138 135138 92.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 25 941 6134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095415
X-RAY DIFFRACTIONf_angle_d0.9817323
X-RAY DIFFRACTIONf_dihedral_angle_d12.1593245
X-RAY DIFFRACTIONf_chiral_restr0.056789
X-RAY DIFFRACTIONf_plane_restr0.007954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.21851740.18963416X-RAY DIFFRACTION74
1.7193-1.73960.22811990.18273767X-RAY DIFFRACTION81
1.7396-1.76080.23422090.18014075X-RAY DIFFRACTION89
1.7608-1.78310.21072280.17454249X-RAY DIFFRACTION92
1.7831-1.80650.22812380.17484496X-RAY DIFFRACTION95
1.8065-1.83130.21322230.16914393X-RAY DIFFRACTION96
1.8313-1.85750.19792330.16494390X-RAY DIFFRACTION95
1.8575-1.88520.19112290.15674377X-RAY DIFFRACTION95
1.8852-1.91460.19092280.14964368X-RAY DIFFRACTION95
1.9146-1.9460.20272300.16064347X-RAY DIFFRACTION95
1.946-1.97960.20092330.16044395X-RAY DIFFRACTION94
1.9796-2.01560.19212230.15454309X-RAY DIFFRACTION94
2.0156-2.05440.16742270.14344323X-RAY DIFFRACTION93
2.0544-2.09630.16792230.14164299X-RAY DIFFRACTION92
2.0963-2.14190.18562230.14014167X-RAY DIFFRACTION90
2.1419-2.19170.18552270.14214360X-RAY DIFFRACTION93
2.1917-2.24650.17622330.13384364X-RAY DIFFRACTION95
2.2465-2.30720.18292300.13754390X-RAY DIFFRACTION95
2.3072-2.37510.1582310.12264366X-RAY DIFFRACTION95
2.3751-2.45180.14912280.12364452X-RAY DIFFRACTION95
2.4518-2.53940.16042280.12144300X-RAY DIFFRACTION94
2.5394-2.64110.17072240.12594363X-RAY DIFFRACTION94
2.6411-2.76120.16942280.12844310X-RAY DIFFRACTION93
2.7612-2.90680.16622250.1344230X-RAY DIFFRACTION92
2.9068-3.08890.17822170.14214159X-RAY DIFFRACTION90
3.0889-3.32730.16792340.13274336X-RAY DIFFRACTION94
3.3273-3.6620.14582320.12634351X-RAY DIFFRACTION94
3.662-4.19150.1542300.11474387X-RAY DIFFRACTION94
4.1915-5.27950.14892290.10654330X-RAY DIFFRACTION93
5.2795-44.27580.14612260.14724327X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.4959-2.21710.31515.92250.21882.060.0148-0.03540.07010.14950.0665-0.08660.0137-0.2008-0.04570.0642-0.00990.03440.14280.02550.059237.601912.3981147.3649
27.36985.81556.99014.59025.50677.03310.1282-0.1717-0.05120.2826-0.0674-0.03030.1212-0.11940.01460.1593-0.002-0.01630.12890.01520.10848.56686.0975155.9388
31.99792.0366-1.9793.1674-4.47027.474-0.0007-0.11320.10630.3944-0.02-0.1671-0.20990.03690.05650.148-0.0118-0.04020.0974-0.01750.129355.875919.7389152.5388
45.7308-0.8623-1.82465.36331.88333.80410.21410.03080.441-0.0927-0.0037-0.1587-0.3198-0.165-0.05650.19-0.03280.0250.09780.00170.076348.054254.805156.9291
52.9578-1.27440.34582.10650.82313.25380.0720.03420.26360.00360.0358-0.2086-0.25130.0431-0.03890.2144-0.02080.06060.0721-0.01150.157147.800356.051155.9468
60.6572-0.41570.12321.0026-0.03270.81450.0217-0.0211-0.03290.117-0.0099-0.02720.0052-0.0338-0.01660.168-0.03750.01080.1139-0.01150.127451.746440.0397157.7498
77.11120.0931-1.41075.1564-0.69785.23460.0009-0.0869-0.3232-0.0757-0.0054-0.30320.12290.39420.11260.15040.0226-0.02470.1444-0.03540.088144.280760.4715117.4331
83.89861.238-0.21473.9989-0.71384.2245-0.12170.1346-0.4135-0.14060.1604-0.25620.35720.36160.0510.17830.01260.00070.1597-0.06170.162143.841356.1039111.2161
90.9730.7839-0.34732.1215-0.40623.7175-0.08280.0943-0.0739-0.09050.1577-0.1430.06570.5253-0.09450.1043-0.019-0.01310.2113-0.03280.130348.499366.0863119.2215
100.97410.207-0.50131.3440.35152.3847-0.026-0.03060.0028-0.031-0.06740.20190.0564-0.21790.04180.1009-0.0112-0.02720.1462-0.01770.136129.815766.0087130.9146
112.18031.1154-1.35391.745-0.61712.8678-0.11050.0703-0.0382-0.11490.02240.09140.1002-0.27370.08670.157-0.0169-0.03490.1426-0.02170.12430.668262.4853122.6983
124.90473.71765.93893.78715.05997.5769-0.22640.21620.2549-0.12860.1460.0278-0.49460.32960.04910.316-0.0542-0.00150.1858-0.00020.122440.287568.5647103.3736
135.22372.3372-2.93136.9199-4.30473.51920.02070.17170.01640.03230.21150.480.7009-0.649-0.12480.2765-0.0687-0.01320.1997-0.01890.161432.256255.5107107.1958
140.3376-0.12420.4950.085-0.17290.7183-0.0251-0.0206-0.01160.1513-0.0182-0.1096-0.0905-0.0170.0420.0574-0.0120.030.14050.00420.09442.164341.921141.5743
151.8813-1.85970.68212.6973-1.20251.08530.0970.0254-0.175-0.17110.0530.0720.18610.0223-0.12690.1046-0.0051-0.00970.1056-0.00240.097949.368210.0729139.7322
161.70972.8233-2.01545.8781-3.59313.7815-0.07290.0652-0.17090.0435-0.1278-0.39150.1360.16210.26850.08140.0091-0.02390.1366-0.00980.147456.052411.3216143.1664
171.42120.40740.0833.6557-0.36783.48890.04670.0921-0.1137-0.0972-0.01470.08660.1267-0.023-0.0310.0979-0.0031-0.00880.078-0.01260.085345.13695.3106138.3515
180.95820.5464-0.48673.2337-1.50081.9307-0.0219-0.02060.09670.1580.16360.269-0.1367-0.184-0.11140.06670.01260.00330.1301-0.00960.105537.378421.2172144.2168
193.2594-3.19670.39294.5601-1.17173.98980.03270.11070.4814-0.09620.02340.2556-0.256-0.2791-0.03310.0953-0.0172-0.03910.12950.02540.276731.828.7077134.5773
202.8166-0.38110.26371.9512-0.13331.6624-0.0390.05340.1245-0.16340.05240.2549-0.0489-0.15910.00850.10940.0058-0.02350.0970.01630.141636.744326.7991135.0887
213.93722.4273-0.76465.8114-1.18598.0154-0.15480.07060.0746-0.10850.1034-0.0969-0.05320.0870.03640.10540.0106-0.00750.0579-0.01290.101544.562934.177138.5383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 204 THROUGH 220 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 221 THROUGH 237 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 238 THROUGH 251 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 26 THROUGH 43 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 44 THROUGH 84 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 85 THROUGH 251 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 27 THROUGH 43 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 44 THROUGH 65 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 66 THROUGH 94 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 95 THROUGH 180 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 181 THROUGH 220 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 221 THROUGH 237 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 238 THROUGH 250 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 1 THROUGH 3 )
15X-RAY DIFFRACTION15CHAIN 'A' AND (RESID 27 THROUGH 43 )
16X-RAY DIFFRACTION16CHAIN 'A' AND (RESID 44 THROUGH 65 )
17X-RAY DIFFRACTION17CHAIN 'A' AND (RESID 66 THROUGH 94 )
18X-RAY DIFFRACTION18CHAIN 'A' AND (RESID 95 THROUGH 128 )
19X-RAY DIFFRACTION19CHAIN 'A' AND (RESID 129 THROUGH 143 )
20X-RAY DIFFRACTION20CHAIN 'A' AND (RESID 144 THROUGH 193 )
21X-RAY DIFFRACTION21CHAIN 'A' AND (RESID 194 THROUGH 203 )

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