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- PDB-4g4p: Crystal structure of glutamine-binding protein from Enterococcus ... -

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Basic information

Entry
Database: PDB / ID: 4g4p
TitleCrystal structure of glutamine-binding protein from Enterococcus faecalis at 1.5 A
ComponentsAmino acid ABC transporter, amino acid-binding/permease protein
KeywordsTRANSPORT PROTEIN / substrate-binding domain / ABC transporter / Glutamine/Glutamate 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: 1.5 Å
AuthorsFulyani, F. / Guskov, A. / Zagar, A.V. / 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
DepositionJul 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Feb 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: Amino acid ABC transporter, amino acid-binding/permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6393
Polymers27,2981
Non-polymers3412
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.730, 61.130, 45.120
Angle α, β, γ (deg.)90.00, 99.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27297.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: EF_0761 / Production host: Escherichia coli (E. coli) / References: UniProt: Q837S0
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


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


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 28% PEG 1500,100 mM MMT, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0098 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2011
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0098 Å / Relative weight: 1
ReflectionResolution: 1.35→44.56 Å / Num. obs: 43037 / % possible obs: 90.6 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 20.4
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 7.4 / % possible all: 57.1

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Processing

Software
NameVersionClassification
MXCUBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→36.008 Å / SU ML: 0.09 / σ(F): 2.08 / Phase error: 12.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.155 1711 5 %
Rwork0.115 --
obs0.1169 34211 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3579 Å20 Å2-0.2843 Å2
2--1.9633 Å20 Å2
3----0.6054 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 22 373 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082057
X-RAY DIFFRACTIONf_angle_d1.2052790
X-RAY DIFFRACTIONf_dihedral_angle_d14.684811
X-RAY DIFFRACTIONf_chiral_restr0.074290
X-RAY DIFFRACTIONf_plane_restr0.006373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54420.13791370.08472603X-RAY DIFFRACTION95
1.5442-1.5940.14681400.08982668X-RAY DIFFRACTION96
1.594-1.6510.15061410.08612679X-RAY DIFFRACTION98
1.651-1.71710.12521430.08972705X-RAY DIFFRACTION98
1.7171-1.79530.1471430.09652716X-RAY DIFFRACTION98
1.7953-1.88990.15121420.1082704X-RAY DIFFRACTION98
1.8899-2.00830.15331430.10442721X-RAY DIFFRACTION98
2.0083-2.16340.1361440.1032734X-RAY DIFFRACTION98
2.1634-2.3810.14541440.11272729X-RAY DIFFRACTION99
2.381-2.72550.18561430.12552721X-RAY DIFFRACTION98
2.7255-3.43340.16631440.13022745X-RAY DIFFRACTION98
3.4334-36.01840.16061470.13352775X-RAY DIFFRACTION98

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