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- PDB-1mor: ISOMERASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 1mor
TitleISOMERASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WITH GLUCOSE 6-PHOSPHATE
ComponentsGLUCOSAMINE 6-PHOSPHATE SYNTHASE
KeywordsGLUTAMINE AMIDOTRANSFERASE
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 / Glucose-6-phosphate isomerase like protein; domain 1 / Nucleophile aminohydrolases, N-terminal / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsTeplyakov, A.
Citation
Journal: Protein Sci. / Year: 1999
Title: The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase.
Authors: Teplyakov, A. / Obmolova, G. / Badet-Denisot, M.A. / Badet, B.
#1: Journal: Protein Sci. / Year: 1999
Title: The Mechanism of Sugar Phosphate Isomerization by Glucosamine 6-Phosphate Synthase
Authors: Teplyakov, A. / Obmolova, G. / Badet-Denisot, M.A. / Badet, B.
#2: Journal: Structure / Year: 1997
Title: Erratum. Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A Crystal Structure of the Glutaminase ...Title: Erratum. Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A 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.
#3: 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 A Crystal Structure of the Glutaminase Domain of ...Title: Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A 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.
#4: 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.
History
DepositionApr 12, 1997Processing site: BNL
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSAMINE 6-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6172
Polymers40,3571
Non-polymers2601
Water4,017223
1
A: GLUCOSAMINE 6-PHOSPHATE SYNTHASE
hetero molecules

A: GLUCOSAMINE 6-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2344
Polymers80,7142
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6250 Å2
ΔGint-17 kcal/mol
Surface area23830 Å2
MethodPISA
2
A: GLUCOSAMINE 6-PHOSPHATE SYNTHASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)243,70312
Polymers242,1426
Non-polymers1,5616
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)146.100, 146.100, 173.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein GLUCOSAMINE 6-PHOSPHATE SYNTHASE / L-GLUTAMINE\:D-FRUCTOSE-6P AMIDOTRANSFERASE


Mass: 40357.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HFR 3000 / Plasmid: PMA200 / Gene (production host): FRAGMENT "ISOMERASE DOMAIN" OF GLMS / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Density % sol: 72 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %MPD11
20.1 MMES11
30.5 Mammonium sulfate11
410 mMFru-6P11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.912
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 28, 1996 / Details: CYLINDRICAL MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 205104 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 1.8 / % possible all: 98.8
Reflection
*PLUS
Num. obs: 55613

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Processing

Software
NameClassification
BLANCmodel building
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
BLANCphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.191 --
obs-55294 99.5 %
Displacement parametersBiso mean: 31.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 16 223 3059
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0310.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.53
X-RAY DIFFRACTIONp_mcangle_it6.36
X-RAY DIFFRACTIONp_scbond_it8.66
X-RAY DIFFRACTIONp_scangle_it11.88
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1110.3
X-RAY DIFFRACTIONp_multtor_nbd0.1750.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.710
X-RAY DIFFRACTIONp_staggered_tor1815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.191 / Rfactor Rfree: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS

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