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- PDB-3kbj: Room temperature X-ray structure of apo-D-Xylose Isomerase -

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Basic information

Entry
Database: PDB / ID: 3kbj
TitleRoom temperature X-ray structure of apo-D-Xylose Isomerase
ComponentsXylose isomerase
KeywordsISOMERASE / apo-form / enzyme / sugar conversion / Carbohydrate metabolism / Metal-binding / Pentose shunt / Xylose metabolism
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 / AB INITIO / Resolution: 2 Å
AuthorsKovalevsky, A.Y. / Hanson, L. / Langan, P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Identification of the Elusive Hydronium Ion Exchanging Roles with a Proton in an Enzyme at Lower pH Values.
Authors: Kovalevsky, A.Y. / Hanson, B.L. / Mason, S.A. / Yoshida, T. / Fisher, S.Z. / Mustyakimov, M. / Forsyth, V.T. / Blakeley, M.P. / Keen, D.A. / Langan, P.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water4,378243
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_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area30110 Å2
ΔGint-104 kcal/mol
Surface area47850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.040, 99.520, 102.470
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-1152-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH / Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / References: UniProt: P24300, xylose isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Source detailsTHE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH

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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: 290 K / pH: 7.7
Details: 40mg/ml protein, 30%(v/v) ammonium sulfate (sat.), pH 7.7, temperature 290K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 32143 / Num. obs: 28999 / % possible obs: 90 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 99.7

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Processing

Software
NameClassification
CrystalCleardata collection
SHELXmodel building
SHELXL-97refinement
CrystalCleardata reduction
CrystalCleardata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 2→10 Å / Num. parameters: 13213 / Num. restraintsaints: 12601 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1600 5 %RANDOM
all0.1865 32143 --
obs0.1837 -98.9 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3263.5
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 0 243 3296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0218
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.081
X-RAY DIFFRACTIONs_approx_iso_adps0

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