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- PDB-1wdn: GLUTAMINE-BINDING PROTEIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1wdn
TitleGLUTAMINE-BINDING PROTEIN
ComponentsGLUTAMINE BINDING PROTEIN
KeywordsCOMPLEX (BINDING PROTEIN/PEPTIDE) / BINDING PROTEIN / GLNBP / CLOSED FORM / COMPLEX / COMPLEX (BINDING PROTEIN-PEPTIDE) / COMPLEX (BINDING PROTEIN-PEPTIDE) complex
Function / homology
Function and homology information


glutamine binding / L-glutamine import across plasma membrane / glutamine transport / ligand-gated monoatomic ion channel activity / amino acid binding / amino acid transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / periplasmic space / membrane
Similarity search - Function
Glutamine-binding periplasmic protein GlnH, type 2 periplasmic binding protein fold / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / 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 ...Glutamine-binding periplasmic protein GlnH, type 2 periplasmic binding protein fold / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / 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-binding periplasmic protein / Glutamine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.94 Å
AuthorsSun, Y.-J. / Rose, J. / Wang, B.-C. / Hsiao, C.-D.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The structure of glutamine-binding protein complexed with glutamine at 1.94 A resolution: comparisons with other amino acid binding proteins.
Authors: Sun, Y.J. / Rose, J. / Wang, B.C. / Hsiao, C.D.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: The Crystal Structure of Glutamine-Binding Protein from Escherichia Coli
Authors: Hsiao, C.D. / Sun, Y.J. / Rose, J. / Wang, B.C.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystals of Glutamine-Binding Protein in Various Conformational States
Authors: Hsiao, C.D. / Sun, Y.J. / Rose, J. / Cottam, P.F. / Ho, C. / Wang, B.C.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary Crystallographic Analysis of Glutamine-Binding Protein from Escherichia Coli
Authors: Chen, P. / Rose, J. / Chung, Y.J. / Wang, B.C. / Shen, Q.C. / Cottam, P.F. / Ho, C.
History
DepositionMay 17, 1997Processing site: BNL
Revision 1.0May 6, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: GLUTAMINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1272
Polymers24,9801
Non-polymers1461
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.700, 91.000, 34.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTAMINE BINDING PROTEIN / GLNBP


Mass: 24980.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: LIGANDED CLOSE-CLEFT FORM / Source: (natural) Escherichia coli (E. coli) / Strain: BK9MDG / References: UniProt: P10344, UniProt: P0AEQ3*PLUS
#2: Chemical ChemComp-GLN / GLUTAMINE


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.11 Å3/Da / Density % sol: 42 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
215 %(w/v)PEG40001drop
3100 mM1dropCdCl2
40.1 Msodium acetate1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 25, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15110 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 65773
Reflection shell
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 2.03 Å / % possible obs: 82.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.94→6 Å / σ(F): 2 /
RfactorNum. reflection
Rfree0.3 -
Rwork0.2 -
obs0.2 12765
Displacement parametersBiso mean: 24.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.94→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 0 122 1862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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