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Basic information

Entry
Database: PDB / ID: 6quf
TitleProtein crystallization by ionic liquid hydrogel support: reference crystal of glucose isomerase grown on standard silanized glass
ComponentsXylose isomerase
KeywordsISOMERASE / Glucose Isomerase / ionic liquid / structural comparison / hydration shell
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. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsBelviso, B.D. / Caliandro, R. / Caliandro, R.
CitationJournal: Crystals / Year: 2019
Title: Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes
Authors: Belviso, B.D. / Caliandro, R. / Salehi, S.M. / di Profio, G. / Caliandro, R.
History
DepositionFeb 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Category: reflns / Item: _reflns.B_iso_Wilson_estimate
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Apr 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.5Jan 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)43,7667
Polymers43,2831
Non-polymers4826
Water9,692538
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)175,06228
Polymers173,1334
Non-polymers1,92924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_757-x+2,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area35480 Å2
ΔGint-222 kcal/mol
Surface area45440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.522, 98.167, 101.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-903-

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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: Protein concentration 26mg/ml in HEPES 10mM pH 7 and MgCl2 1mM. reservoir: (NH4)2SO4 1.5M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97779 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 1.19→39.93 Å / Num. obs: 112879 / % possible obs: 76.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 8.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.03 / Rrim(I) all: 0.049 / Net I/σ(I): 14.7
Reflection shellResolution: 1.19→1.22 Å / Redundancy: 1 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 522 / CC1/2: 0.966 / Rpim(I) all: 0.166 / Rrim(I) all: 0.234 / % possible all: 4.9

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Processing

Software
NameVersionClassification
xia2data reduction
Aimlessdata scaling
Sir2014phasing
REFMAC5.8.0238refinement
BUSTER-TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAD

1oad


Resolution: 1.19→39.93 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.979 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12943 5749 5.1 %RANDOM
Rwork0.10659 ---
obs0.10775 107045 76.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.397 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.07 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.19→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 25 538 3596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133285
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172994
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.6494466
X-RAY DIFFRACTIONr_angle_other_deg1.5171.5846926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14620.783217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64215529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6041538
X-RAY DIFFRACTIONr_chiral_restr0.0630.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023838
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02785
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.9680.9621601
X-RAY DIFFRACTIONr_mcbond_other6.9660.961600
X-RAY DIFFRACTIONr_mcangle_it8.5711.4532013
X-RAY DIFFRACTIONr_mcangle_other8.5731.4542014
X-RAY DIFFRACTIONr_scbond_it10.1861.421684
X-RAY DIFFRACTIONr_scbond_other10.1891.4221685
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.8451.9682441
X-RAY DIFFRACTIONr_long_range_B_refined15.2613.9553976
X-RAY DIFFRACTIONr_long_range_B_other15.34113.1013833
X-RAY DIFFRACTIONr_rigid_bond_restr26.14136276
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.191→1.222 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 26 -
Rwork0.243 500 -
obs--4.87 %

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