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

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Entry
Database: PDB / ID: 1mos
TitleISOMERASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WITH 2-AMINO-2-DEOXYGLUCITOL 6-PHOSPHATE
ComponentsGLUCOSAMINE 6-PHOSPHATE SYNTHASE
KeywordsTRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / AMINOTRANSFERASE
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 / Nucleophile aminohydrolases, N-terminal / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2 Å
AuthorsTeplyakov, A. / Obmolova, G. / Badet-Denisot, M.A. / Badet, B.
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: Structure / Year: 1998
Title: Involvement of the C Terminus in Intramolecular Nitrogen Channeling in Glucosamine 6-Phosphate Synthase: Evidence from a 1.6 A Crystal Structure of the Isomerase Domain
Authors: Teplyakov, A. / Obmolova, G. / Badet-Denisot, M.A. / Badet, B. / Polikarpov, I.
#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
DepositionJul 15, 1998Processing site: BNL
Revision 1.0Jul 29, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSAMINE 6-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1257
Polymers40,3571
Non-polymers7686
Water3,243180
1
A: GLUCOSAMINE 6-PHOSPHATE SYNTHASE
hetero molecules

A: GLUCOSAMINE 6-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,24914
Polymers80,7142
Non-polymers1,53512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8750 Å2
ΔGint-118 kcal/mol
Surface area23550 Å2
MethodPISA
2
A: GLUCOSAMINE 6-PHOSPHATE SYNTHASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)246,74842
Polymers242,1426
Non-polymers4,60536
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)143.900, 143.900, 172.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-612-

SO4

21A-156-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 40357.004 Da / Num. of mol.: 1 / Fragment: ISOMERASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 3000HFR / Plasmid: PMA200 / Gene (production host): GLMS / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing)

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Non-polymers , 5 types, 186 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-AGP / 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE


Mass: 261.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16NO8P
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 4.3 Å3/Da / Density % sol: 71 %
Crystal growpH: 6 / Details: pH 6.00
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 mMligand11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 45840 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 3.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.6 / % possible all: 95.7
Reflection
*PLUS
Num. obs: 45848
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1MOQ

1moq


Resolution: 2→12 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 -5 %RANDOM
obs0.244 45626 98.7 %-
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 44 180 3048
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0260.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it6.24
X-RAY DIFFRACTIONp_mcangle_it7.36
X-RAY DIFFRACTIONp_scbond_it8.56
X-RAY DIFFRACTIONp_scangle_it10.88
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.1590.15
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_tor3.510
X-RAY DIFFRACTIONp_staggered_tor1815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.248 / Rfactor Rfree: 0.286
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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