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- PDB-6quk: Protein crystallization by ionic liquid hydrogel support: glucose... -

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Basic information

Entry
Database: PDB / ID: 6quk
TitleProtein crystallization by ionic liquid hydrogel support: glucose isomerase grown by using ionic liquid hydrogel
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: 1.58 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 / reflns_shell
Item: _reflns.B_iso_Wilson_estimate / _reflns_shell.Rmerge_I_obs
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 18, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Sep 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 1.5Apr 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.6Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,71516
Polymers86,5672
Non-polymers1,14914
Water16,736929
1
A: Xylose isomerase
B: Xylose isomerase
hetero molecules

A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,43032
Polymers173,1334
Non-polymers2,29728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area36450 Å2
ΔGint-210 kcal/mol
Surface area45230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.900, 92.598, 99.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

21B-848-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: protein 26mg/m 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: 1.58→64.9 Å / Num. obs: 103356 / % possible obs: 95.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 9.6 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.07 / Rrim(I) all: 0.115 / Net I/σ(I): 11.1
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7748 / CC1/2: 0.622 / Rpim(I) all: 0.492 / Rrim(I) all: 0.791 / % possible all: 97.4

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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: 1.58→62.98 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.84 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19449 5269 5.1 %RANDOM
Rwork0.16682 ---
obs0.16824 97718 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.58→62.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 62 929 7057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126383
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175825
X-RAY DIFFRACTIONr_angle_refined_deg0.6351.648641
X-RAY DIFFRACTIONr_angle_other_deg0.2361.56713428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9935796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4720.594421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.841151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8861575
X-RAY DIFFRACTIONr_chiral_restr0.0440.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027397
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021536
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_it0.930.9673118
X-RAY DIFFRACTIONr_mcbond_other0.9160.9663117
X-RAY DIFFRACTIONr_mcangle_it1.3891.4483906
X-RAY DIFFRACTIONr_mcangle_other1.3941.4493907
X-RAY DIFFRACTIONr_scbond_it2.0181.2243265
X-RAY DIFFRACTIONr_scbond_other2.0181.2243266
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0741.754726
X-RAY DIFFRACTIONr_long_range_B_refined4.90913.3877794
X-RAY DIFFRACTIONr_long_range_B_other4.72313.0077689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 408 -
Rwork0.28 7250 -
obs--96.04 %

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