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- PDB-8fdb: CRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM Shewanel... -

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Basic information

Entry
Database: PDB / ID: 8fdb
TitleCRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM Shewanella denitrificans OS217 IN COMPLEX WITH GLUCITOLAMINE-6-PHOSPHATE AT 3.06 A RESOLUTION.
Components(Glutamine-fructose-6-phosphate transaminase ...) x 2
KeywordsISOMERASE / Deaminase Isomerization-deamination Amino-sugar metabolism Positive cooperativity and allosteric activation Sugar-isomerase domain
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/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily
Similarity search - Domain/homology
2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE / Glutamine-fructose-6-phosphate transaminase (Isomerizing)
Similarity search - Component
Biological speciesShewanella denitrificans OS217 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsRodriguez-Romero, A. / Rodriguez-Hernandez, A. / Marcos-Viquez, J. / Bustos-Jaimes, I.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CF2019 87163 Mexico
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
DepositionDec 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine-fructose-6-phosphate transaminase (Isomerizing)
B: Glutamine-fructose-6-phosphate transaminase (Isomerizing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,27410
Polymers70,9972
Non-polymers1,2778
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-68 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.885, 113.142, 171.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Glutamine-fructose-6-phosphate transaminase ... , 2 types, 2 molecules AB

#1: Protein Glutamine-fructose-6-phosphate transaminase (Isomerizing)


Mass: 35476.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Strain: OS217 / ATCC BAA-1090 / DSM 15013 / Gene: Sden_2705 / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / References: UniProt: Q12KP2
#2: Protein Glutamine-fructose-6-phosphate transaminase (Isomerizing)


Mass: 35519.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Gene: Sden_2705 / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / References: UniProt: Q12KP2

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Non-polymers , 4 types, 24 molecules

#3: Chemical
ChemComp-AGP / 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE


Mass: 261.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H16NO8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.86 % / Description: Bypyramidal plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50mM Tris-HCl, pH 8.5, with 1mM 2-deoxi-2-amino glucitol 6-phosphate (GlcNol6P)

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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 17, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 3→49.48 Å / Num. obs: 14320 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 45.49 Å2 / CC1/2: 0.794 / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.8
Reflection shellResolution: 3.06→3.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3 / Num. unique obs: 2383 / CC1/2: 0.89 / Rpim(I) all: 0.25 / Χ2: 0.82 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BALBES

Resolution: 3.06→34.95 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 1093 8.16 %
Rwork0.2059 --
obs0.2089 13389 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.06→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 78 16 5010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065062
X-RAY DIFFRACTIONf_angle_d1.1846888
X-RAY DIFFRACTIONf_dihedral_angle_d5.39738
X-RAY DIFFRACTIONf_chiral_restr0.07853
X-RAY DIFFRACTIONf_plane_restr0.01873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.20.35931220.2731520X-RAY DIFFRACTION99
3.2-3.370.27691420.23521508X-RAY DIFFRACTION100
3.37-3.580.26091320.22181533X-RAY DIFFRACTION100
3.58-3.850.31371320.23411492X-RAY DIFFRACTION98
3.85-4.240.21491440.19921536X-RAY DIFFRACTION99
4.24-4.850.2091340.17921508X-RAY DIFFRACTION98
4.85-6.110.24231410.20241579X-RAY DIFFRACTION100
6.11-34.950.17551460.16761620X-RAY DIFFRACTION99

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