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- PDB-3qza: Joint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9 -

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Basic information

Entry
Database: PDB / ID: 3qza
TitleJoint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9
ComponentsXylose isomerase
KeywordsISOMERASE / joint X-ray/neutron structure / TIM barrel / xylose / cytosol
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: 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
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.3Jun 6, 2018Group: Data collection / Experimental preparation / Refinement description
Category: exptl_crystal_grow / software / Item: _exptl_crystal_grow.method
Revision 1.4Mar 13, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.5Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2852
Polymers43,2831
Non-polymers21
Water4,756264
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)173,1418
Polymers173,1334
Non-polymers84
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 area31580 Å2
ΔGint-195 kcal/mol
Surface area47300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.908, 99.503, 102.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-D8U / deuterium(1+)


Mass: 2.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: D
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: D2O
Nonpolymer detailsTHE DEUTERON ION IS COMPLEXED BY FOUR CARBOXYLIC ACIDS AND DOES NOT COVALENTLY BIND ANY OF THEM. ...THE DEUTERON ION IS COMPLEXED BY FOUR CARBOXYLIC ACIDS AND DOES NOT COVALENTLY BIND ANY OF THEM. THIS IS SIMILAR TO HYDROGEN COMPLEXATION AS REVIEWED BY CHAMBERON & MEYER, CHEM. SOC. REV., 2009, 38, 1663-1673.

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 280 K / Method: batch mode / pH: 5.9
Details: crystals grew with ammonium sulfate as a precipitant at pH of 5.9, batch crystallization, temperature 280K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORLANSCE PCS10.6-7.0
ROTATING ANODERIGAKU FR-E+ DW21.5418
Detector
TypeIDDetectorDate
position sensitive He31AREA DETECTORSep 15, 2010
RIGAKU RAXIS IV++2IMAGE PLATEJun 14, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1noTOF LAUELneutron1
2graphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.61
271
31.54181
Reflection

Entry-ID: 3QZA

Resolution (Å)Num. allNum. obs% possible obs (%)Observed criterion σ(F)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-28.46282902829086.92.21.530.22514.5
1.7-29.86530875308799.2003.2220.07728.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2-2.111.70.3851.30.385171.5
1.7-1.762.880.3152.60.315296.5

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Processing

Software
NameVersionClassificationNB
nCNS1.0.0refinement
d*TREKdata scaling
d*TREK(X-ray)data reduction
LAUENORM(Neutron)data reduction
LAUENORM(Neutron)data scaling
Refinement

Biso max: 72.85 Å2 / Biso min: 9.03 Å2 / Rfactor obs: 0.254 / % reflection Rfree: 5 % / R Free selection details: RANDOM / Data cutoff high rms absF: 2.2 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: PDB ENTRY 2GUB

2gub

/ Stereochemistry target values: joint XN ML / Solvent model: CNS bulk solvent model used / Bsol: 39.4577 Å2 / ksol: 0.287656 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection obs (%)Diffraction-IDσ(F)
2-20NEUTRON DIFFRACTION0.280.0040.2541347282902676081.412.2
1.7-20X-RAY DIFFRACTION0.2110.0050.19525074980593.622.5
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.16 Å
Luzzati d res high-1.7
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 0 264 3318
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.007
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_dihedral_angle_d17.9
NEUTRON DIFFRACTIONx_improper_angle_d0.82
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d17.9
X-RAY DIFFRACTIONx_improper_angle_d0.82

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