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- PDB-8eol: CRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM SHEWANEL... -

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Basic information

Entry
Database: PDB / ID: 8eol
TitleCRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM SHEWANELLA DENITRIFICANS OS217 AT 2.17 A RESOLUTION
ComponentsGLUCOSAMINE-6-PHOSPHATE DEAMINASE
KeywordsISOMERASE / GLUCOSAMINE-6_PHOSPHATE DEAMINASE Isomerase Apo form
Function / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / carbohydrate derivative metabolic process / carbohydrate derivative binding / cytoplasm
Similarity search - Function
GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamine-fructose-6-phosphate transaminase (Isomerizing)
Similarity search - Component
Biological speciesShewanella denitrificans OS217 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsRodriguez-Hernandez, A. / Marcos-Viquez, J. / Rodriguez-Romero, A. / Bustos-Jaimes, I.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)315896 Mexico
CitationJournal: Protein Sci. / Year: 2023
Title: Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS-fold glucosamine-6-phosphate deaminases.
Authors: Marcos-Viquez, J. / Rodriguez-Hernandez, A. / Alvarez-Anorve, L.I. / Medina-Garcia, A. / Plumbridge, J. / Calcagno, M.L. / Rodriguez-Romero, A. / Bustos-Jaimes, I.
History
DepositionOct 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSAMINE-6-PHOSPHATE DEAMINASE
B: GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Theoretical massNumber of molelcules
Total (without water)70,9542
Polymers70,9542
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-15 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.378, 78.746, 96.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUCOSAMINE-6-PHOSPHATE DEAMINASE


Mass: 35476.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: No density was observed for three regions of the polypeptide chain A: Residues 50 to 54 Residues 243-254 Residues 323-334
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Plasmid: PET24B / Production host: Escherichia coli (E. coli) / Strain (production host): 469008 / References: UniProt: Q12KP2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris, pH 8.5, 30% w/v PEG 4000. Crystals grew in the presence of 1mM GlcNAc6P; however, no density for the ligand was observed in the electron density maps.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.17→41.2588 Å / Num. obs: 29534 / % possible obs: 98.54 % / Redundancy: 11 % / CC1/2: 0.931 / Net I/σ(I): 2.8
Reflection shellResolution: 2.17→2.24 Å / Num. unique obs: 2539 / CC1/2: 0.931

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure with ligands GNPDA-GlcNol6P

Resolution: 2.17→41.251 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.51 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1491 5.05 %
Rwork0.1882 --
obs0.1904 29534 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→41.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 0 204 4609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014483
X-RAY DIFFRACTIONf_angle_d1.0256110
X-RAY DIFFRACTIONf_dihedral_angle_d2.2883650
X-RAY DIFFRACTIONf_chiral_restr0.06760
X-RAY DIFFRACTIONf_plane_restr0.007783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.240.28311340.20572539X-RAY DIFFRACTION100
2.24-2.32010.27051340.20832558X-RAY DIFFRACTION99
2.3201-2.4130.25051340.21262506X-RAY DIFFRACTION99
2.413-2.52280.31851360.22032515X-RAY DIFFRACTION99
2.5228-2.65580.28031310.222506X-RAY DIFFRACTION98
2.6558-2.82210.30391230.2232498X-RAY DIFFRACTION97
2.8221-3.040.27881330.21762508X-RAY DIFFRACTION97
3.04-3.34580.25551300.20082548X-RAY DIFFRACTION99
3.3458-3.82960.22981510.17512574X-RAY DIFFRACTION100
3.8296-4.82370.16951450.15152591X-RAY DIFFRACTION99
4.8237-41.2510.18771400.17282700X-RAY DIFFRACTION98

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