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- PDB-3kbv: Room temperature structure of D-Xylose Isomerase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3kbv
TitleRoom temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors
ComponentsXylose isomerase
KeywordsISOMERASE / xylose isomerase / 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
NICKEL (II) ION / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 1.8 Å
AuthorsKovalevsky, A.Y. / Hanson, L. / Langan, P.
CitationJournal: Structure / Year: 2010
Title: Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Authors: Kovalevsky, A.Y. / Hanson, L. / Fisher, S.Z. / Mustyakimov, M. / Mason, S.A. / Forsyth, V.T. / Blakeley, M.P. / Keen, D.A. / Wagner, T. / Carrell, H.L. / Katz, A.K. / Glusker, J.P. / Langan, P.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4013
Polymers43,2831
Non-polymers1172
Water4,035224
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)173,60312
Polymers173,1334
Non-polymers4708
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 area30470 Å2
ΔGint-114 kcal/mol
Surface area47430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.990, 99.470, 102.960
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-1136-

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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 290 K / Method: batch / pH: 7.7
Details: 40mg/ml protein, 5mM NiCl2, 30% (v/v) ammonium sulfate (sat.), pH 7.7, batch, 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: Oct 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 44836 / Num. obs: 41073 / % possible obs: 92 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.88 Å / % possible all: 95

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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: 1.8→20 Å / Num. parameters: 13113 / Num. restraintsaints: 12510 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 2235 5 %RANDOM
all0.1836 44836 --
obs0.1811 -99.7 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3275.5
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 2 224 3279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0224
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.074
X-RAY DIFFRACTIONs_approx_iso_adps0

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