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- PDB-6ybr: RT structure of Glucose Isomerase obtained at 1.20 A resolution f... -

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Basic information

Entry
Database: PDB / ID: 6ybr
TitleRT structure of Glucose Isomerase obtained at 1.20 A resolution from crystal grown in a Mylar microchip.
ComponentsXylose isomerase
KeywordsISOMERASE / XYLOSE ISOMERASE
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / 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: 1.2 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

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3785
Polymers43,2831
Non-polymers954
Water5,242291
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,51220
Polymers173,1334
Non-polymers37816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
Buried area32420 Å2
ΔGint-280 kcal/mol
Surface area46110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.990, 99.380, 103.100
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-513-

HOH

21A-675-

HOH

31A-749-

HOH

41A-755-

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.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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

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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: 1.2→46.99 Å / Num. obs: 149874 / % possible obs: 99.95 % / Redundancy: 8.86 % / Biso Wilson estimate: 16.95 Å2 / CC1/2: 0.994 / Net I/σ(I): 17
Reflection shellResolution: 1.2→1.24 Å / Num. unique obs: 14856 / CC1/2: 0.41

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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: 1.2→46.99 Å / SU ML: 0.1343 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.6927
RfactorNum. reflection% reflection
Rfree0.1305 7490 5 %
Rwork0.121 --
obs0.1215 149841 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.93 Å2
Refinement stepCycle: LAST / Resolution: 1.2→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 4 291 3328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473517
X-RAY DIFFRACTIONf_angle_d0.88874817
X-RAY DIFFRACTIONf_chiral_restr0.0747485
X-RAY DIFFRACTIONf_plane_restr0.0066680
X-RAY DIFFRACTIONf_dihedral_angle_d8.58621951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.33262440.35644639X-RAY DIFFRACTION99.49
1.21-1.230.31362490.31654724X-RAY DIFFRACTION99.76
1.23-1.240.26452490.27084725X-RAY DIFFRACTION99.9
1.24-1.260.27542480.26024714X-RAY DIFFRACTION99.96
1.26-1.280.30672460.31284676X-RAY DIFFRACTION99.96
1.28-1.290.31332480.28284709X-RAY DIFFRACTION99.96
1.29-1.310.22312470.23764693X-RAY DIFFRACTION99.94
1.31-1.330.19612480.18684723X-RAY DIFFRACTION100
1.33-1.350.1782480.1594714X-RAY DIFFRACTION99.98
1.35-1.370.14022490.1364722X-RAY DIFFRACTION99.98
1.37-1.40.12582490.11414729X-RAY DIFFRACTION100
1.4-1.420.12242480.10534709X-RAY DIFFRACTION99.98
1.42-1.450.11932490.10054732X-RAY DIFFRACTION99.98
1.45-1.480.11862480.0974715X-RAY DIFFRACTION99.96
1.48-1.510.1122470.09644710X-RAY DIFFRACTION99.96
1.51-1.550.11622490.09534731X-RAY DIFFRACTION100
1.55-1.590.10892500.09434755X-RAY DIFFRACTION100
1.59-1.630.10342490.08874731X-RAY DIFFRACTION100
1.63-1.680.10582500.08274741X-RAY DIFFRACTION100
1.68-1.730.09642480.08954715X-RAY DIFFRACTION100
1.73-1.790.10972500.09174750X-RAY DIFFRACTION99.96
1.79-1.860.11232500.09664756X-RAY DIFFRACTION100
1.86-1.950.10562510.09634763X-RAY DIFFRACTION100
1.95-2.050.10582500.09974752X-RAY DIFFRACTION100
2.05-2.180.12092510.10874763X-RAY DIFFRACTION100
2.18-2.350.11372510.11074776X-RAY DIFFRACTION100
2.35-2.590.13422530.12424816X-RAY DIFFRACTION100
2.59-2.960.1352530.12984808X-RAY DIFFRACTION100
2.96-3.730.12342560.12094848X-RAY DIFFRACTION100
3.73-46.990.14082620.12735012X-RAY DIFFRACTION99.87

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