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- PDB-1jxa: GLUCOSAMINE 6-PHOSPHATE SYNTHASE WITH GLUCOSE 6-PHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1jxa
TitleGLUCOSAMINE 6-PHOSPHATE SYNTHASE WITH GLUCOSE 6-PHOSPHATE
Componentsglucosamine 6-phosphate synthase
KeywordsTRANSFERASE / beta-sandwich / nucleotide-binding fold / gene duplication / ammonia channel
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 / protein N-linked glycosylation / fructose 6-phosphate metabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUCOSE-6-PHOSPHATE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTeplyakov, A. / Obmolova, G. / Badet, B. / Badet-Denisot, M.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Channeling of ammonia in glucosamine-6-phosphate synthase.
Authors: Teplyakov, A. / Obmolova, G. / Badet, B. / Badet-Denisot, M.A.
History
DepositionSep 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 16, 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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glucosamine 6-phosphate synthase
B: glucosamine 6-phosphate synthase
C: glucosamine 6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,9745
Polymers200,4543
Non-polymers5202
Water70339
1
A: glucosamine 6-phosphate synthase
hetero molecules

A: glucosamine 6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1564
Polymers133,6362
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: glucosamine 6-phosphate synthase
C: glucosamine 6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8963
Polymers133,6362
Non-polymers2601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-14 kcal/mol
Surface area41700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.400, 112.400, 185.100
Angle α, β, γ (deg.)90.00, 96.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of one biological homodimer is generated by the two-fold axis (-x, y, -z) applied to chain A. Another dimer is formed by chains B and C.

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Components

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


Mass: 66818.000 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical ChemComp-G6Q / GLUCOSE-6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: LiCl, PEG4K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: Obmolova, G., (1994) J.Mol.Biol., 242, 703.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 MHEPES1drop
31 M1dropLiCl
43 %(w/v)PEG40001drop
510 mMFru6P1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 8, 1998 / Details: CYLINDRICAL MIRROR
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 45685 / Num. obs: 45685 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 74.5 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 2.8 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 111045

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Processing

Software
NameClassification
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOQ, 1GDO

1moq

1gdo
PDB Unreleased entry


Resolution: 3.1→12 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2280 5 %random
Rwork0.2 ---
all0.22 45607 --
obs0.22 45607 --
Refinement stepCycle: LAST / Resolution: 3.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14085 0 32 39 14156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d1.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.22 / Rfactor obs: 0.2 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5

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