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- PDB-2vf4: E. coli glucosamine-6-P synthase -

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Basic information

Entry
Database: PDB / ID: 2vf4
TitleE. coli glucosamine-6-P synthase
ComponentsGLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE
KeywordsTRANSFERASE / AMIDOTRANSFERASE / AMMONIA CHANNELING / N TERMINAL NUCLEOPHILE / GLUTAMINE AMIDOTRANSFERASE / AMINOTRANSFERASE / GLUCOSAMINE 6-PHOSPHATE SYNTHASE
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/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
Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMouilleron, S. / Golinelli-Pimpaneau, B.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Ordering of C-Terminal Loop and Glutaminase Domains of Glucosamine-6-Phosphate Synthase Promotes Sugar Ring Opening and Formation of the Ammonia Channel.
Authors: Mouilleron, S. / Badet-Denisot, M.-A. / Golinelli-Pimpaneau, B.
History
DepositionOct 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Dec 13, 2023Group: Refinement description / Structure summary / Category: audit_author / pdbx_initial_refinement_model / Item: _audit_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)66,8461
Polymers66,8461
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)144.704, 144.704, 171.779
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--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE / HEXOSEPHOSPHATE AMINOTRANSFERASE / D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE / GFAT / L-GLUTAMINE-D- ...HEXOSEPHOSPHATE AMINOTRANSFERASE / D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE / GFAT / L-GLUTAMINE-D-FRUCTOSE-6-PHOSPHATEAMIDOTRANSFERASE / GLUCOSAMINE-6-PHOSPHATE SYNTHASE / GLUCOSAMINE-6-P SYNTHASE


Mass: 66846.016 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101
References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.58 Å3/Da / Density % sol: 52.4 % / Description: NONE
Crystal growpH: 5.3
Details: 7% PEG 4000, 70 MM SODIUM ACETATE PH 5.3, 30% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.95→20 Å / Num. obs: 13948 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 6.3
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOQ

1moq


Resolution: 2.95→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.998 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.662 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DISORDERED GLUTAMINASE DOMAIN WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 740 5.1 %RANDOM
Rwork0.219 ---
obs0.22 13874 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 0 11 2780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212821
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3091.9743819
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9615358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1440.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022094
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2910.21540
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5621.51782
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02322862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7831039
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8624.5957
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.02 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 60
Rwork0.232 956
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.76080.0570.89453.3581-1.53644.0807-0.18740.37280.2961-0.093-0.2954-0.7461-1.00461.84260.48280.6619-0.6593-0.18111.11980.20510.538835.494227.65215.1545
22.4324-0.08460.19912.4830.55984.0959-0.0657-0.41640.08190.2829-0.10420.0848-0.4380.35350.170.1958-0.1716-0.08430.16230.08780.199414.662916.296312.8362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X243 - 449
2X-RAY DIFFRACTION2X450 - 601

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