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- PDB-2gve: Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase -

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Basic information

Entry
Database: PDB / ID: 2gve
TitleTime-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase
ComponentsXylose isomerase
KeywordsISOMERASE / TIM barrel-beta-alpha-barrels / two metal binding sites / protonation states of residues
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
: / DEUTERATED WATER / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKatz, A.K. / Li, X. / Carrell, H.L. / Hanson, B.L. / Langan, P. / Coates, L. / Schoenborn, B.P. / Glusker, J.P. / Bunick, G.J.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction.
Authors: Katz, A.K. / Li, X. / Carrell, H.L. / Hanson, B.L. / Langan, P. / Coates, L. / Schoenborn, B.P. / Glusker, J.P. / Bunick, G.J.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1994
Title: Modes of binding substrates and their analogs to the enzyme D-xylose isomerase
Authors: Carrell, H.L. / Hoier, H. / Glusker, J.P.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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-polymers1182
Water9,224512
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)173,60512
Polymers173,1334
Non-polymers4718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area32780 Å2
ΔGint-300 kcal/mol
Surface area45560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.880, 99.680, 102.900
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-1094-

DOD

21A-1269-

DOD

31A-1279-

DOD

41A-3335-

DOD

Detailshomo-tetramer consisting of subunits related by crystallographic 222 symmetry

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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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 8
Details: 50mM tris-HCl,38%AMSO4,2mM Mn2+ and 2mM Co2+,XI @ 125mg/ml, pH 8.0, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 0.7-7.0
DetectorType: Time-of-Flight Multiwire He3 neutron detector / Detector: AREA DETECTOR / Date: Sep 15, 2003
RadiationMonochromator: chopper / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
271
ReflectionResolution: 1.8→20 Å / Num. all: 34394 / Num. obs: 34394 / % possible obs: 78 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5 / Rsym value: 0.185
Reflection shellResolution: 1.8→1.94 Å / Num. unique all: 3692 / Rsym value: 0.262 / % possible all: 39

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Processing

Software
NameVersionClassification
d*TREKmodified for neutron time-of-flight lauedata reduction
SHELXL-97model building
SHELXL-97refinement
d*TREKMODIFIED FOR NEUTRON TIME-OF-FLIGHT LAUEdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XIB

1xib


Resolution: 2.2→10 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.319 1184 5%, Random
Rwork0.268 --
obs0.271 23312 -
all-23312 -
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 2 512 3568
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONs_bond_d0.032
NEUTRON DIFFRACTIONs_zero_chiral_vol0.036
NEUTRON DIFFRACTIONs_non_zero_chiral_vol0.055
NEUTRON DIFFRACTIONs_anti_bump_dis_restr0.168
NEUTRON DIFFRACTIONs_angle_d0.173

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