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

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Basic information

Entry
Database: PDB / ID: 2put
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
ACETATE ION / FRUCTOSE -6-PHOSPHATE / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Aug 30, 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 / diffrn_source / 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_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_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)
C: isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
D: isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,13918
Polymers162,4594
Non-polymers3,68014
Water13,475748
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.028, 118.188, 100.032
Angle α, β, γ (deg.)90.00, 91.78, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains the tetrameric biological assembly

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4 / 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)

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Non-polymers , 5 types, 762 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Chemical
ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 30% v/v 2-methyl-2,4-pentanediol, 10-fold excess of UDP-GlcNAc and Glc-6-P; crystals soaked with large excess of Fru-6-P, VAPOR ...Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 30% v/v 2-methyl-2,4-pentanediol, 10-fold excess of UDP-GlcNAc and Glc-6-P; crystals soaked with large excess of Fru-6-P, 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: 0.8162 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 9, 2006
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8162 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 120651 / Num. obs: 120651 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 5965 / Rsym value: 0.569 / % possible all: 98.4

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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: 1.9→19.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.984 / SU ML: 0.089 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21508 2419 2 %RANDOM
Rwork0.17074 ---
all0.17165 120111 --
obs0.17165 117692 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: 25.584 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati sigma a obs: 0.0892 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10705 0 232 748 11685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02211204
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.99315180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60751401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02623.889468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.524152019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8961584
X-RAY DIFFRACTIONr_chiral_restr0.1150.21802
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028124
X-RAY DIFFRACTIONr_nbd_refined0.2170.25602
X-RAY DIFFRACTIONr_nbtor_refined0.3070.27890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2946
X-RAY DIFFRACTIONr_metal_ion_refined0.110.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0350.22
X-RAY DIFFRACTIONr_mcbond_it1.0541.56903
X-RAY DIFFRACTIONr_mcangle_it1.86211181
X-RAY DIFFRACTIONr_scbond_it2.89234376
X-RAY DIFFRACTIONr_scangle_it4.6184.53985
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 182 -
Rwork0.214 8504 -
obs-8504 100 %

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