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- PDB-4dvo: Room-temperature joint X-ray/neutron structure of D-xylose isomer... -

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Basic information

Entry
Database: PDB / ID: 4dvo
TitleRoom-temperature joint X-ray/neutron structure of D-xylose isomerase in complex with 2Ni2+ and per-deuterated D-sorbitol at pH 5.9
ComponentsXylose isomerase
KeywordsISOMERASE / TIM-barrel
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 / NICKEL (II) ION / sorbitol / 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: Acta Crystallogr.,Sect.D / Year: 2012
Title: Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography.
Authors: Kovalevsky, A. / Hanson, B.L. / Mason, S.A. / Forsyth, V.T. / Fisher, Z. / Mustyakimov, M. / Blakeley, M.P. / Keen, D.A. / Langan, P.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6425
Polymers43,2831
Non-polymers3584
Water5,188288
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)174,56620
Polymers173,1334
Non-polymers1,43316
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 area32420 Å2
ΔGint-302 kcal/mol
Surface area46780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.061, 99.428, 102.798
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-1101-

DOD

21A-1162-

DOD

31A-1256-

DOD

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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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O6
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: D2O

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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: 55.7 %
Crystal growTemperature: 290 K / Method: batch / pH: 5.9
Details: apo-Xylose isomerase crystals were grown with AmSO4 as precipitant and 0.1 M MES at pH 5.9; they then were injected with Ni2+ salt up to the concentration of 5mM and D-sorbitol up to the ...Details: apo-Xylose isomerase crystals were grown with AmSO4 as precipitant and 0.1 M MES at pH 5.9; they then were injected with Ni2+ salt up to the concentration of 5mM and D-sorbitol up to the concentration of 300mM, batch, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORD1912.422
ROTATING ANODERIGAKU FR-E DW21.54
Detector
TypeIDDetectorDate
He3-filled PSD1AREA DETECTORJul 15, 2010
RIGAKU RAXIS IV++2IMAGE PLATEApr 5, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMneutron1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.4221
21.541
Reflection

Entry-ID: 4DVO

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(F)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-49.723058593240.15417.6
1.55-29.96821497.53.220.07229.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.12.40.4081.8190
1.55-1.612.660.3472.6293.5

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Processing

Software
NameClassification
CNSrefinement
nCNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1501 5 %RANDOM
Rwork0.19 ---
obs0.19 30162 91.8 %-
all-30585 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 15 288 3357
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.006
NEUTRON DIFFRACTIONc_angle_deg0.92

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