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- PDB-2puw: The crystal structure of isomerase domain of glucosamine-6-phosph... -

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Basic information

Entry
Database: PDB / ID: 2puw
TitleThe crystal structure of isomerase domain of glucosamine-6-phosphate synthase from Candida albicans
Componentsisomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
KeywordsTRANSFERASE / glucosamine-6-phosphate synthase / aldose/ketose isomerase / crystal structure / Rossmann-like fold
Function / homology
Function and homology information


glucosamine biosynthetic process / hyphal growth / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / chitin biosynthetic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding / protein N-linked glycosylation / fructose 6-phosphate metabolic process
Similarity search - Function
: / 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 ...: / 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
6-O-phosphono-beta-D-glucopyranose / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.151 Å
AuthorsRaczynska, J. / Olchowy, J. / Milewski, S. / Rypniewski, W.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Crystal and Solution Studies of Glucosamine-6-phosphate Synthase from Candida albicans
Authors: Raczynska, J. / Olchowy, J. / Konariev, P.V. / Svergun, D.I. / Milewski, S. / Rypniewski, W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and preliminary X-ray analysis of the isomerase domain of glucosamine-6-phosphate synthase from Candida albicans
Authors: Olchowy, J. / Jedrzejczak, R. / Milewski, S. / Rypniewski, W.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
B: isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8216
Polymers81,2292
Non-polymers5914
Water00
1
A: isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
B: isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
hetero molecules

A: isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
B: isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,64112
Polymers162,4594
Non-polymers1,1828
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)148.864, 148.864, 102.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing) / E.C.2.6.1.16 / Hexosephosphate aminotransferase / D-fructose-6- phosphate amidotransferase / GFAT


Mass: 40614.738 Da / Num. of mol.: 2 / Fragment: isomerase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / Gene: GFA1 / Plasmid: pET23b-FRU / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P53704, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% w/v PEG 600, 0.15M KSCN, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8125 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 5, 2003
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8125 Å / Relative weight: 1
ReflectionResolution: 3.151→20 Å / Num. all: 19526 / Num. obs: 19526 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 70 Å2 / Rsym value: 0.195 / Net I/σ(I): 7.7
Reflection shellResolution: 3.151→3.2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 971 / Rsym value: 0.79 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POC

2poc


Resolution: 3.151→19.55 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.864 / SU B: 25.518 / SU ML: 0.401 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27948 399 2.1 %RANDOM
Rwork0.22988 ---
all0.23096 19427 --
obs0.23096 19028 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.835 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refine analyzeLuzzati sigma a obs: 0.4003 Å
Refinement stepCycle: LAST / Resolution: 3.151→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 34 0 5235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225310
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9797174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8775664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93123.964222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.63915962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4431538
X-RAY DIFFRACTIONr_chiral_restr0.0980.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023850
X-RAY DIFFRACTIONr_nbd_refined0.2580.22927
X-RAY DIFFRACTIONr_nbtor_refined0.320.23662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.27
X-RAY DIFFRACTIONr_mcbond_it0.5721.53390
X-RAY DIFFRACTIONr_mcangle_it1.03725380
X-RAY DIFFRACTIONr_scbond_it1.10632103
X-RAY DIFFRACTIONr_scangle_it1.9694.51794
LS refinement shellResolution: 3.151→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 27 -
Rwork0.337 1388 -
obs-1388 100 %

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