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- PDB-1xfg: Glutaminase domain of glucosamine 6-phosphate synthase complexed ... -

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Basic information

Entry
Database: PDB / ID: 1xfg
TitleGlutaminase domain of glucosamine 6-phosphate synthase complexed with l-glu hydroxamate
ComponentsGlucosamine--fructose-6-phosphate aminotransferase [isomerizing]
KeywordsTRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / N-TERMINAL NUCLEOPHILE
Function / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. / SIS domain superfamily / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GLUTAMINE HYDROXAMATE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsIsupov, M.N. / Teplyakov, A.
Citation
Journal: Structure / Year: 1996
Title: Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 Angstrom Crystal Structure of the Glutaminase Domain ...Title: Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 Angstrom Crystal Structure of the Glutaminase Domain of Glucosamine 6-Phosphate Synthase
Authors: Isupov, M.N. / Obmolova, G. / Butterworth, S. / Badet-Denisot, M.-A. / Badet, B. / Polikarpov, I. / Littlechild, J.A. / Teplyakov, A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of the Two Domains of Glucosamine-6-Phosphate Synthase from Escherichia Coli
Authors: Obmolova, G. / Badet-Denisot, M.A. / Badet, B. / Teplyakov, A.
#2: Journal: J.Mol.Biol. / Year: 2001
Title: Channeling of Ammonia in Glucosamine 6-Phosphate Synthase
Authors: Teplyakov, A. / Obmolova, G. / Badet-Denisot, M.A. / Badet, B.
History
DepositionSep 14, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionSep 28, 2004ID: 1GMS
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Database references / Category: diffrn_source / struct_ref
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
B: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4437
Polymers53,0142
Non-polymers4295
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.250, 82.400, 85.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] / E.C.2.6.1.16 / Hexosephosphate aminotransferase / D-fructose-6-phosphate amidotransferase / GFAT / L-glutamine-D- ...Hexosephosphate aminotransferase / D-fructose-6-phosphate amidotransferase / GFAT / L-glutamine-D-fructose-6-phosphate amidotransferase / Glucosamine-6-phosphate synthase


Mass: 26507.059 Da / Num. of mol.: 2 / Fragment: GLUTAMINASE DOMAIN
Source method: isolated from a genetically manipulated source
Details: inhibited by L-GLUTAMATE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 3000HFR / Gene: GLMS / Plasmid: PGM10A / Production host: Escherichia coli (E. coli)
References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-HGA / GLUTAMINE HYDROXAMATE


Mass: 162.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.34 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M cacodylate, 1 M sodium acetate, 20% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93 / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 1993 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.85→15 Å / Num. all: 42930 / Num. obs: 42930 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.2
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 3.2 / % possible all: 92.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPH

1gph


Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.974 / SU B: 1.829 / SU ML: 0.056 / Cross valid method: none used / σ(F): 0 / ESU R: 0.114
RfactorNum. reflection% reflection
Rwork0.159 --
all0.159 42930 -
obs0.159 42930 99.6 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.72 Å20 Å2
3----0.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.114 Å / Luzzati sigma a obs: 0.056 Å
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 32 295 4022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213786
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9465122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.455475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98423.039181
X-RAY DIFFRACTIONr_chiral_restr0.1270.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022889
X-RAY DIFFRACTIONr_nbd_refined0.2460.21757
X-RAY DIFFRACTIONr_nbtor_refined0.3310.22673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2376
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.215
X-RAY DIFFRACTIONr_mcbond_it5.02642366
X-RAY DIFFRACTIONr_mcangle_it7.25693788
X-RAY DIFFRACTIONr_scbond_it10.12591445
X-RAY DIFFRACTIONr_scangle_it12.94791334
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.183 3008 -
Rfree-0 -
obs-3008 92.3 %

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