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

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Basic information

Entry
Database: PDB / ID: 8eym
TitleCRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM SHEWANELLA DENITRIFICANS OS217 IN COMPLEX WITH GLUCITOLAMINE-6-PHOSPHATE AND N-ACETYLGLUCOSAMINE-6-PHOSPHATE AT 2.31 A RESOLUTION
ComponentsGLUCOSAMINE-6-PHOSPHATE DEAMINASE
KeywordsISOMERASE / GLUCOSAMINE-6_PHOSPHATE DEAMINASE ISOMERASE SHEWANELLA DENITRIFICANS
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
Chem-16G / 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: 2.311 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 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0796
Polymers70,9542
Non-polymers1,1254
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-41 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.181, 80.237, 91.508
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 the first two residues (MET & THR) and the last 12 residues due to disorder.
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Plasmid: PET24B / Production host: Escherichia coli (E. coli) / Strain (production host): 469008 / References: UniProt: Q12KP2
#2: Sugar ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / N-acetyl-6-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-AGP / 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE


Mass: 261.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16NO8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 0.25 M Tris-HCl pH 8.5, 30% w/v PEG 4000. Crystals containing GlcNol6P and GlcNAc6P grew in the presence of 1 mM GlcNAc6P and were soaked in the crystallization drop with 1 mM ...Details: 0.2 M MgCl2, 0.25 M Tris-HCl pH 8.5, 30% w/v PEG 4000. Crystals containing GlcNol6P and GlcNAc6P grew in the presence of 1 mM GlcNAc6P and were soaked in the crystallization drop with 1 mM GlcNol6P five minutes before freezing for data collection.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.31→39.75 Å / Num. obs: 22873 / % possible obs: 94.41 % / Redundancy: 4.6 % / CC1/2: 0.945 / Net I/σ(I): 36.1
Reflection shellResolution: 2.31→2.35 Å / Rmerge(I) obs: 0.223 / Num. unique obs: 2757

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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: SdNagBII-GlcNol6P

Resolution: 2.311→39.746 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 998 4.36 %
Rwork0.1856 --
obs0.1877 22873 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.311→39.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 70 177 4955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084857
X-RAY DIFFRACTIONf_angle_d1.0566629
X-RAY DIFFRACTIONf_dihedral_angle_d6.0133438
X-RAY DIFFRACTIONf_chiral_restr0.078831
X-RAY DIFFRACTIONf_plane_restr0.007839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.311-2.43250.35221250.24352757X-RAY DIFFRACTION85
2.4325-2.58490.2551350.23582933X-RAY DIFFRACTION90
2.5849-2.78440.28831390.23633048X-RAY DIFFRACTION93
2.7844-3.06460.25351410.2223135X-RAY DIFFRACTION96
3.0646-3.50780.26311490.19413236X-RAY DIFFRACTION98
3.5078-4.41850.19631510.15463303X-RAY DIFFRACTION99
4.4185-390.2031580.15973463X-RAY DIFFRACTION99

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