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- PDB-4zb2: A native form of glucose isomerase collected at room temperature. -

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Basic information

Entry
Database: PDB / ID: 4zb2
TitleA native form of glucose isomerase collected at room temperature.
ComponentsXylose isomerase
KeywordsISOMERASE
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
beta-D-fructofuranose / alpha-D-glucopyranose / : / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSandy, J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: A generic protocol for protein crystal dehydration using the HC1b humidity controller.
Authors: Lobley, C.M. / Sandy, J. / Sanchez-Weatherby, J. / Mazzorana, M. / Krojer, T. / Nowak, R.P. / Sorensen, T.L.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.name ..._atom_site.occupancy / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)43,7535
Polymers43,2831
Non-polymers4704
Water5,423301
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)175,01420
Polymers173,1334
Non-polymers1,88116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area34990 Å2
ΔGint-130 kcal/mol
Surface area45920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.074, 99.225, 103.034
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-748-

HOH

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Components

#1: Protein Xylose isomerase / Glucose Isomerase


Mass: 43283.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: 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: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Hepes, 10% PEG 400, 0.05 M Manganese Chloride, 20% Glucose

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Data collection

DiffractionMean temperature: 293 K
Ambient temp details: Collected using HC1b Humidity Control Device at RH of 96%
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→69.47 Å / Num. obs: 32817 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 12.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
xia2xia2/dialsdata reduction
xia2xia2/dialsdata scaling
MOLREP11.3.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MNZ

1mnz


Resolution: 2→69.47 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.082 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13985 1701 5.2 %RANDOM
Rwork0.10585 ---
obs0.10769 31116 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.462 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2--0.48 Å20 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 2→69.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 26 301 3372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193185
X-RAY DIFFRACTIONr_bond_other_d0.0020.022955
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.9584318
X-RAY DIFFRACTIONr_angle_other_deg1.14436771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3915398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53822.832173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66715502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2181538
X-RAY DIFFRACTIONr_chiral_restr0.1360.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213692
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02794
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_it2.0081.4991559
X-RAY DIFFRACTIONr_mcbond_other2.0091.4941558
X-RAY DIFFRACTIONr_mcangle_it2.9222.231950
X-RAY DIFFRACTIONr_mcangle_other2.9292.2361951
X-RAY DIFFRACTIONr_scbond_it3.5481.9581626
X-RAY DIFFRACTIONr_scbond_other3.5411.9581626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5412.7712363
X-RAY DIFFRACTIONr_long_range_B_refined7.48213.6923907
X-RAY DIFFRACTIONr_long_range_B_other7.48113.6913907
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 101 -
Rwork0.117 2292 -
obs--99.58 %

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