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- PDB-3kcj: Room temperature neutron structure of apo-D-Xylose Isomerase (ref... -

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Basic information

Entry
Database: PDB / ID: 3kcj
TitleRoom temperature neutron structure of apo-D-Xylose Isomerase (refined jointly with X-ray structure 3KBJ)
ComponentsXylose isomerase
KeywordsISOMERASE / D-xylose isomerase / apo-form / Carbohydrate metabolism / Metal-binding / Pentose shunt / Xylose metabolism
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / 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
DEUTERATED WATER / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKovalevsky, A.Y. / 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 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Data collection
Revision 1.3Aug 17, 2011Group: Database references
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Feb 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
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
Water4,288238
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 area31640 Å2
ΔGint-190 kcal/mol
Surface area46710 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-

DOD

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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
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: D2O
Source detailsTHE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / pH: 7.7
Details: 50MM HEPES, 40% v/v (NH4)2SO4 (sat.), protein 40 MG/ML, PH 7.7, BATCH METHOD, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceBeamlineIDWavelength (Å)
NUCLEAR REACTORD1912.422
ROTATING ANODE21.54
Detector
TypeIDDetectorDate
POSITION-SENSITIVE HE3 NEUTRON DETECTOR1AREA DETECTORApr 15, 2009
RIGAKU RAXIS IV++2IMAGE PLATEFeb 15, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMneutron1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.4221
21.541
ReflectionResolution: 1.8→20 Å / Num. all: 39080 / Num. obs: 29152 / % possible obs: 75 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1.6
Reflection shellResolution: 1.8→1.9 Å / % possible all: 72.6

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Processing

Software
NameClassification
nCNSrefinement
RETREATdata reduction
RETREATdata scaling
nCNSphasing
Refinement

R Free selection details: RANDOM / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 3CWH

3cwh

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection Rfree (%)Diffraction-IDStereochemistry target values
1.8-20NEUTRON DIFFRACTION0.1810.173120939080291524.11ENGH AND HUBER
2-20X-RAY DIFFRACTION0.1870.17915465.12
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 0 238 3292
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.006
NEUTRON DIFFRACTIONc_angle_deg0.946

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