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- PDB-4kpt: Crystal structure of substrate binding domain 1 (SBD1) OF ABC tra... -

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Basic information

Entry
Database: PDB / ID: 4kpt
TitleCrystal structure of substrate binding domain 1 (SBD1) OF ABC transporter GLNPQ from lactococcus lactis
ComponentsGlutamine ABC transporter permease and substrate binding protein protein
KeywordsTRANSPORT PROTEIN / GLUTAMINE BINDING PROTEIN / AMINO ACID TRANSPORT / EXTRACELLULAR
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. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ETE / DI(HYDROXYETHYL)ETHER / 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: 1.4 Å
AuthorsVujicic Zagar, A. / Guskov, A. / Schuurman-Wolters, G.K. / Slotboom, D.J. / Poolman, B.
CitationJournal: Structure / Year: 2013
Title: Functional Diversity of Tandem Substrate-Binding Domains in ABC Transporters from Pathogenic Bacteria.
Authors: Fulyani, F. / Schuurman-Wolters, G.K. / Zagar, A.V. / Guskov, A. / Slotboom, D.J. / Poolman, B.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)57,70021
Polymers54,6102
Non-polymers3,09019
Water9,314517
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A: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,29913
Polymers27,3051
Non-polymers1,99312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4018
Polymers27,3051
Non-polymers1,0967
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.100, 55.629, 55.735
Angle α, β, γ (deg.)93.99, 89.71, 97.98
Int Tables number1
Space group name H-MP1

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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: 27305.184 Da / Num. of mol.: 2 / Fragment: SUBSTRATE BINDING DOMAIN 1, UNP residues 1-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Strain: IL1403 / Gene: glnP, L165, LL1759 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CES5

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Non-polymers , 6 types, 536 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*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-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40% PEG 400, 5% PEG 3000, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.4→17.943 Å / Num. all: 81996 / Num. obs: 76748 / % possible obs: 93.5 % / Observed criterion σ(I): 1.5
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.5 / % possible all: 92.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→17.943 Å / SU ML: 0.14 / σ(F): 1.96 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 3857 5.03 %RANDOM
Rwork0.1395 ---
obs0.1419 76731 93.59 %-
all-76731 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→17.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 198 517 4127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093789
X-RAY DIFFRACTIONf_angle_d1.2455069
X-RAY DIFFRACTIONf_dihedral_angle_d15.3781495
X-RAY DIFFRACTIONf_chiral_restr0.068534
X-RAY DIFFRACTIONf_plane_restr0.006631
LS refinement shellResolution: 1.4→1.4171 Å
RfactorNum. reflection% reflection
Rfree0.2594 161 -
Rwork0.2285 2489 -
obs--93 %

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