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- PDB-6ybo: RT structure of Glucose Isomerase obtained at 1.06 A resolution f... -

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Basic information

Entry
Database: PDB / ID: 6ybo
TitleRT structure of Glucose Isomerase obtained at 1.06 A resolution from crystal grown in a Kapton microchip.
ComponentsXylose isomerase
KeywordsISOMERASE / D-XYLOSE KETOL ISOMERASE
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2016-74875-P Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips.
Authors: Gavira, J.A. / Rodriguez-Ruiz, I. / Martinez-Rodriguez, S. / Basu, S. / Teychene, S. / McCarthy, A.A. / Mueller-Dieckman, C.
History
DepositionMar 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3554
Polymers43,2831
Non-polymers723
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-32 kcal/mol
Surface area19110 Å2
Unit cell
Length a, b, c (Å)93.940, 99.370, 103.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

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Components

#1: Protein Xylose isomerase /


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293.5 K / Method: counter-diffusion / pH: 7 / Details: 0.1 M MgCl2, 10% w/v PEG 1K, 0.1 M Hepes pH 7.0 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 293.5 K / Ambient temp details: Room Temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2017
Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.06→41.12 Å / Num. obs: 200000 / % possible obs: 92.32 % / Redundancy: 7.93 % / Biso Wilson estimate: 13.05 Å2 / CC1/2: 0.987 / Net I/σ(I): 8.4
Reflection shellResolution: 1.06→1.09 Å / Num. unique obs: 8688 / CC1/2: 0.614 / % possible all: 40.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
PHASERphasing
PHENIX1.15.2_3472refinement
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A8I

4a8i


Resolution: 1.06→41.12 Å / SU ML: 0.091 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.0028
RfactorNum. reflection% reflection
Rfree0.131 9998 5 %
Rwork0.1229 --
obs0.1233 199958 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.18 Å2
Refinement stepCycle: LAST / Resolution: 1.06→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 3 281 3317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463567
X-RAY DIFFRACTIONf_angle_d0.90414900
X-RAY DIFFRACTIONf_chiral_restr0.0754494
X-RAY DIFFRACTIONf_plane_restr0.007690
X-RAY DIFFRACTIONf_dihedral_angle_d7.56132532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.070.40021230.36932340X-RAY DIFFRACTION34.35
1.07-1.080.42831450.37932730X-RAY DIFFRACTION39.96
1.08-1.10.31931660.34933160X-RAY DIFFRACTION46.36
1.1-1.110.34832760.33385231X-RAY DIFFRACTION77
1.11-1.130.353030.32035775X-RAY DIFFRACTION84.9
1.13-1.140.27173230.25596137X-RAY DIFFRACTION90.15
1.14-1.160.22573500.21826645X-RAY DIFFRACTION97.45
1.16-1.180.18823540.19186745X-RAY DIFFRACTION99.34
1.18-1.190.18563570.17486796X-RAY DIFFRACTION99.83
1.19-1.210.1753570.16686782X-RAY DIFFRACTION99.8
1.21-1.230.15543600.15686833X-RAY DIFFRACTION99.81
1.23-1.260.15523600.14256848X-RAY DIFFRACTION99.9
1.26-1.280.14273570.13236778X-RAY DIFFRACTION99.94
1.28-1.310.1343590.12546814X-RAY DIFFRACTION99.92
1.31-1.340.11843600.11126849X-RAY DIFFRACTION99.97
1.34-1.370.12183590.10896818X-RAY DIFFRACTION100
1.37-1.40.11333610.10386851X-RAY DIFFRACTION99.96
1.4-1.440.12763590.0956828X-RAY DIFFRACTION99.99
1.44-1.480.10093610.08696857X-RAY DIFFRACTION100
1.48-1.530.08653610.0836860X-RAY DIFFRACTION100
1.53-1.580.09163610.08286864X-RAY DIFFRACTION99.99
1.58-1.650.09293610.08526858X-RAY DIFFRACTION100
1.65-1.720.10523600.09256847X-RAY DIFFRACTION99.97
1.72-1.810.10483620.09786868X-RAY DIFFRACTION100
1.81-1.930.11063620.09956875X-RAY DIFFRACTION100
1.93-2.070.10483640.10036919X-RAY DIFFRACTION100
2.07-2.280.11213640.10546912X-RAY DIFFRACTION100
2.28-2.610.12973650.12166948X-RAY DIFFRACTION100
2.61-3.290.13533690.12927007X-RAY DIFFRACTION100
3.29-41.120.13543790.12887185X-RAY DIFFRACTION99.95

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