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- PDB-6h30: The crystal structure of SBD1-SBD2 tandem of GlnPQ transporter -

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Basic information

Entry
Database: PDB / ID: 6h30
TitleThe crystal structure of SBD1-SBD2 tandem of GlnPQ transporter
ComponentsGlutamine ABC transporter permease and substrate binding protein protein
KeywordsTRANSPORT PROTEIN / GLUTAMINE BINDING PROTEIN / AMINO ACID TRANSPORT
Function / homology
Function and homology information


peptide transport / ligand-gated monoatomic ion channel activity / ATP-binding cassette (ABC) transporter complex / protein transport
Similarity search - Function
Amino acid ABC transporter, permease protein, 3-TM domain / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / 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 / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamine ABC transporter permease and substrate binding protein protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchuurman-Wolters, G.K. / Guskov, A. / Poolman, B.
CitationJournal: To Be Published
Title: The crystal structure of SBD1-SBD2 tandem of GlnPQ transporter
Authors: Schuurman-Wolters, G.K. / Guskov, A. / Poolman, B.
History
DepositionJul 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine ABC transporter permease and substrate binding protein protein
B: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,42849
Polymers100,6612
Non-polymers6,76747
Water4,216234
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A: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,01833
Polymers50,3301
Non-polymers4,68732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,41016
Polymers50,3301
Non-polymers2,07915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.560, 187.033, 134.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamine ABC transporter permease and substrate binding protein protein


Mass: 50330.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GM at the N-terminus is the cloning artefact
Source: (gene. exp.) Lactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
Gene: glnP, L165 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CES5

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Non-polymers , 7 types, 281 molecules

#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 125 mM MES pH 6.0, 25 % PEG200, 6.25% PEG3350 and 50 mM NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 29326 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 4
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100

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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

4kpt


Resolution: 2.8→19.974 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.94
RfactorNum. reflection% reflection
Rfree0.2399 1490 5.08 %
Rwork0.1638 --
obs0.1676 29325 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 445 234 7689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087582
X-RAY DIFFRACTIONf_angle_d1.06310075
X-RAY DIFFRACTIONf_dihedral_angle_d15.1564519
X-RAY DIFFRACTIONf_chiral_restr0.0551046
X-RAY DIFFRACTIONf_plane_restr0.0071253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89020.36011430.27332476X-RAY DIFFRACTION100
2.8902-2.99310.32111430.24632518X-RAY DIFFRACTION100
2.9931-3.11250.29761260.2152491X-RAY DIFFRACTION100
3.1125-3.25360.28551350.20842486X-RAY DIFFRACTION100
3.2536-3.42440.29941490.18872493X-RAY DIFFRACTION100
3.4244-3.63770.24271080.16622540X-RAY DIFFRACTION100
3.6377-3.91660.23061390.14842530X-RAY DIFFRACTION100
3.9166-4.30720.19281410.13242527X-RAY DIFFRACTION100
4.3072-4.92230.21721360.12472541X-RAY DIFFRACTION100
4.9223-6.17110.19841500.14172557X-RAY DIFFRACTION100
6.1711-19.97430.20781200.15232676X-RAY DIFFRACTION100
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)
13.01061.2810.11482.4506-0.22140.9951-0.0770.20370.1453-0.10480.0128-0.0665-0.0088-0.01120.05650.34680.0671-0.00420.33130.06730.2975-56.1679-57.105878.8535
23.9249-0.87880.62820.975-0.18711.07770.12890.1044-0.1336-0.0525-0.082-0.17940.14240.1666-0.05170.39620.0155-0.00650.2714-0.0180.293-22.2761-77.639890.6142
33.7399-2.28870.30154.945-0.67441.4870.03810.33170.0027-0.2845-0.04790.19370.17210.0050.00840.3903-0.08620.03750.33770.01090.2989-17.5095-65.891356.0228
42.51951.15581.9264-0.27880.70761.31940.34151.761-0.7010.04690.163-0.16640.10980.47320.03390.58830.0845-0.01921.0234-0.26240.6728-55.459-78.629650.9446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 261 )
2X-RAY DIFFRACTION2chain 'A' and (resid 262 through 483 )
3X-RAY DIFFRACTION3chain 'B' and (resid 29 through 237 )
4X-RAY DIFFRACTION4chain 'B' and (resid 238 through 481 )

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