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- PDB-2gub: Crystal Structure of Metal Free D-Xylose Isomerase. -

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Basic information

Entry
Database: PDB / ID: 2gub
TitleCrystal Structure of Metal Free D-Xylose Isomerase.
ComponentsXylose isomerase
KeywordsISOMERASE / TIM barrel / beta-alpha-barrel / metal-free / inactive enzyme / sugar interconversion
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
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsCarrell, H.L. / Katz, A.K. / Glusker, J.P.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction.
Authors: Katz, A.K. / Li, X. / Carrell, H.L. / Hanson, B.L. / Langan, P. / Coates, L. / Schoenborn, B.P. / Glusker, J.P. / Bunick, G.J.
#1: Journal: To be Published
Title: Structural studies of D-Xylose isomerase and metal binding.
Authors: Carrell, H.L. / Katz, A.K. / Glusker, J.P.
History
DepositionApr 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)43,2831
Polymers43,2831
Non-polymers00
Water6,738374
1
A: Xylose isomerase

A: Xylose isomerase

A: Xylose isomerase

A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)173,1334
Polymers173,1334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area30320 Å2
ΔGint-101 kcal/mol
Surface area46050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.800, 99.500, 102.800
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-485-

HOH

21A-660-

HOH

31A-712-

HOH

Detailshomo-tetramer consisting of subunits related by crystallographic 222 symmetry.

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Purified enzyme obtained as gift from Clinton Corn Products, Clinton, Ia.
Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 279 K / Method: small tubes / pH: 8
Details: Crystallization from solution containing metal free enzyme at 20 mg/ml, 0.8M AmSO4, 2mM Pipes. Crystallization occurred over 2 day period in sealed tubes., pH 8.0, SMALL TUBES, temperature 279K

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Nov 15, 1995 / Details: focussing nickel mirrors
RadiationMonochromator: Focussed Ni Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→70.71 Å / Num. obs: 40569 / % possible obs: 0.83 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.9 Å / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DATCOLdata reduction
XDSdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1XIB without metal ions and solvent

1xib


Resolution: 1.8→70.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.119 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19327 2121 5 %RANDOM
Rwork0.15958 ---
obs0.16124 40237 93.79 %-
all-40569 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 0 374 3407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213109
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9524207
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46522.976168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33115493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0951535
X-RAY DIFFRACTIONr_chiral_restr0.1520.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022480
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21339
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.273
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2351.51950
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80223026
X-RAY DIFFRACTIONr_scbond_it3.28131295
X-RAY DIFFRACTIONr_scangle_it5.1924.51181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 141 -
Rwork0.289 2578 -
obs-2578 82.39 %

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