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- PDB-4kqp: Crystal structure of Lactococcus lactis GlnP substrate binding do... -

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Basic information

Entry
Database: PDB / ID: 4kqp
TitleCrystal structure of Lactococcus lactis GlnP substrate binding domain 2 (SBD2) in complex with glutamine at 0.95 A resolution
ComponentsGlutamine ABC transporter permease and substrate binding protein protein
KeywordsTRANSPORT PROTEIN / GLUTAMINE/GLUTAMIC ACID BINDING / 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
GLUTAMINE / 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: 0.95 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 15, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6162
Polymers25,4691
Non-polymers1461
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.990, 51.690, 44.230
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25469.373 Da / Num. of mol.: 1 / Fragment: SUBSTRATE BINDING DOMAIN 2, UNP residues 255-484
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
#2: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% PEG 6000, 100MM CACL2, 0.1M SODIUM ACETATE BUFFER, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 0.95→44.2 Å / Num. all: 121679 / Num. obs: 119821 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.8
Reflection shellResolution: 0.95→1 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.24 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→44.2 Å / SU ML: 0.06 / σ(F): 1.99 / Phase error: 9.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1197 5990 5 %RANDOM
Rwork0.1147 ---
obs0.1149 119814 98.46 %-
all-119821 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.95→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 10 440 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072085
X-RAY DIFFRACTIONf_angle_d1.2812852
X-RAY DIFFRACTIONf_dihedral_angle_d11.768791
X-RAY DIFFRACTIONf_chiral_restr0.07309
X-RAY DIFFRACTIONf_plane_restr0.007375
LS refinement shellResolution: 0.95→0.9608 Å
RfactorNum. reflection% reflection
Rfree0.2049 195 -
Rwork0.2073 3717 -
obs--96 %

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