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

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Basic information

Entry
Database: PDB / ID: 2poc
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 / 6-O-phosphono-beta-D-glucopyranose / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRaczynska, J. / Olchowy, J. / Milewski, S. / Rypniewski, W.
CitationJournal: 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.
History
DepositionApr 26, 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 1.3Apr 15, 2020Group: Data collection / Category: diffrn_source / reflns / reflns_shell
Item: _diffrn_source.pdbx_synchrotron_site / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 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

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
Water16,069892
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.977, 117.832, 99.711
Angle α, β, γ (deg.)90.00, 91.60, 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 / Sugars , 2 types, 8 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)
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 902 molecules

#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
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;, 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: Mar 16, 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: 1.8→20 Å / Num. all: 141467 / Num. obs: 141467 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.07 / Net I/σ(I): 20.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.549 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOQ

1moq


Resolution: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.402 / SU ML: 0.076 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NULLf
RfactorNum. reflection% reflectionSelection details
Rfree0.20641 2819 2 %RANDOM
Rwork0.17469 ---
obs0.17533 137699 100 %-
all-140518 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.247 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati sigma a0.1105 Å0.1155 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10707 0 232 892 11831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02211211
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.99515196
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58451392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7823.945469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.527152017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7441582
X-RAY DIFFRACTIONr_chiral_restr0.1150.21815
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028098
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.25748
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.27879
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21078
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0380.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0411.56899
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.814211184
X-RAY DIFFRACTIONr_scbond_it2.8434386
X-RAY DIFFRACTIONr_scangle_it4.5444.54004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 189 -
Rwork0.221 10136 -
obs--100 %

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