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- PDB-4kr5: Crystal structure of Lactococcus lactis GlnP substrate binding do... -

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Basic information

Entry
Database: PDB / ID: 4kr5
TitleCrystal structure of Lactococcus lactis GlnP substrate binding domain 2 (SBD2) in open conformation
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
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: 1.5 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 16, 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,42514
Polymers50,9392
Non-polymers1,48612
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-37 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.691, 89.123, 59.477
Angle α, β, γ (deg.)90.00, 95.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-628-

HOH

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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: 25469.373 Da / Num. of mol.: 2 / Fragment: SUBSTRATE BINDING DOMAIN 2
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 , 8 types, 766 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#7: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#8: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 46.44 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 40% PEG 6000, 0.1M SODIUM ACETATE BUFFER, 200MM MGCL2, 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: 1.5→19.9 Å / Num. all: 73385 / Num. obs: 72578 / % possible obs: 98.9 % / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.04 / Net I/σ(I): 1.7
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.7 / % possible all: 98

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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: 1.5→19.89 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 3654 5.04 %RANDOM
Rwork0.1434 ---
obs0.1456 72554 98.74 %-
all-72578 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 85 754 4405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093932
X-RAY DIFFRACTIONf_angle_d1.2895340
X-RAY DIFFRACTIONf_dihedral_angle_d13.651516
X-RAY DIFFRACTIONf_chiral_restr0.08565
X-RAY DIFFRACTIONf_plane_restr0.006687
LS refinement shellResolution: 1.5→1.5197 Å
RfactorNum. reflection% reflection
Rfree0.3711 145 -
Rwork0.3116 2590 -
obs--97 %

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