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- PDB-1ggg: GLUTAMINE BINDING PROTEIN OPEN LIGAND-FREE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1ggg
TitleGLUTAMINE BINDING PROTEIN OPEN LIGAND-FREE STRUCTURE
ComponentsGLUTAMINE BINDING PROTEIN
KeywordsBINDING PROTEIN / AMINO-ACID TRANSPORT / GLNBP / OPEN FORM
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-binding periplasmic protein / Glutamine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / ISIRAS / Resolution: 2.3 Å
AuthorsHsiao, C.-D. / Sun, Y.-J. / Rose, J. / Wang, B.-C.
Citation
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.
#1: 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.
#2: 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
DepositionJun 25, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMINE BINDING PROTEIN
B: GLUTAMINE BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,9612
Polymers49,9612
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.300, 86.300, 81.500
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.: 2
Source method: isolated from a genetically manipulated source
Details: THIS ENTRY REPRESENTS THE OPEN LIGAND FREE STRUCTURE
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BK9MDG / Production host: Escherichia coli (E. coli) / References: UniProt: P10344, UniProt: P0AEQ3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENTRY REPRESENTS THE LIGAND FREE "OPEN" FORM OF THE PROTEIN. UPON BINDING L-GLN, THE PROTEIN ...THIS ENTRY REPRESENTS THE LIGAND FREE "OPEN" FORM OF THE PROTEIN. UPON BINDING L-GLN, THE PROTEIN UNDERGOES A LARGE CONFORMATIONAL CHANGE RESULTING IN WHAT IS TERMED THE LIGAND BOUND "CLOSED FORM" CONFORMATION.

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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: 3.04 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.6 / Details: pH 8.6
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MTris-HCl1drop
350 %satammonium sulfate1drop
475 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 25, 1990 / Details: SUPPER MIRRORS
RadiationMonochromator: NI FOIL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→48.5 Å / Num. obs: 24247 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.0513 / Net I/σ(I): 17.37
Reflection shellResolution: 2.3→2.46 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.2511 / Mean I/σ(I) obs: 2.045 / % possible all: 61
Reflection
*PLUS
Num. measured all: 100231

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Processing

Software
NameVersionClassification
ISIRphasing
X-PLOR3.1refinement
XENGENV. 2.0data reduction
XENGENV. 2.0data scaling
RefinementMethod to determine structure: ISIRAS / Resolution: 2.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.289 -10 %
Rwork0.203 --
obs0.203 23800 81 %
Displacement parametersBiso mean: 24.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 0 159 3746
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.5
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 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 21735
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % reflection Rfree: 0.37 % / Total num. of bins used: 8 / Num. reflection obs: 782 / Rfactor obs: 0.32

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