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- PDB-4zef: Crystal structure of substrate binding domain 2 (SBD2) OF ABC tra... -

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Basic information

Entry
Database: PDB / ID: 4zef
TitleCrystal structure of substrate binding domain 2 (SBD2) OF ABC transporter GLNPQ from Enterococcus faecalis
ComponentsAmino acid ABC transporter amino acid-binding/permease
KeywordsTRANSPORT PROTEIN / ATP-Binding Cassette Transporter / substrate binding / glutamine binding
Function / homology
Function and homology information


nitrogen compound transport / ligand-gated monoatomic ion channel activity / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Amino acid ABC transporter, permease protein, 3-TM domain / 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. ...Amino acid ABC transporter, permease protein, 3-TM domain / 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 / Amino acid ABC transporter, amino acid-binding/permease protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFulyani, F. / Guskov, A. / Poolman, B.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWO Netherlands
CitationJournal: To Be Published
Title: Crystal structure of substrate binding domain 2 (SBD2) OF ABC transporter GLNPQ from Enterococcus faecalis
Authors: Fulyani, F. / Guskov, A. / Poolman, B.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amino acid ABC transporter amino acid-binding/permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2582
Polymers28,1121
Non-polymers1461
Water5,531307
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.140, 81.140, 102.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Amino acid ABC transporter amino acid-binding/permease / amino acid-binding/permease protein


Mass: 28111.789 Da / Num. of mol.: 1 / Fragment: residues 266-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: EF_0761, I574_01170, OO5_02671 / Production host: Escherichia coli (E. coli) / References: UniProt: Q837S0
#2: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


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


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M potassium sodium tartrate, 0.1 M Na citrate, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / 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: 1.4→50 Å / Num. obs: 67836 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.6
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.26 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KQP

4kqp


Resolution: 1.4→43.294 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1584 3389 5 %Random selection
Rwork0.1286 ---
obs0.1301 67753 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→43.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 10 307 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092061
X-RAY DIFFRACTIONf_angle_d1.2272790
X-RAY DIFFRACTIONf_dihedral_angle_d13.275795
X-RAY DIFFRACTIONf_chiral_restr0.077291
X-RAY DIFFRACTIONf_plane_restr0.006374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3999-1.41990.341380.31932634X-RAY DIFFRACTION100
3.2047-4.03710.12841460.11532775X-RAY DIFFRACTION100

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