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- PDB-8xia: X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZ... -

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Basic information

Entry
Database: PDB / ID: 8xia
TitleX-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
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
: / D-xylose / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsCarrell, H.L. / Glusker, J.P.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator.
Authors: Carrell, H.L. / Glusker, J.P. / Burger, V. / Manfre, F. / Tritsch, D. / Biellmann, J.F.
#1: Journal: Protein Eng. / Year: 1987
Title: Comparison of Backbone Structures of Glucose Isomerase from Streptomyces and Arthrobacter
Authors: Henrick, K. / Blow, D.M. / Carrell, H.L. / Glusker, J.P.
#2: Journal: J.Biol.Chem. / Year: 1984
Title: X-Ray Crystal Structure of D-Xylose Isomerase at 4-Angstroms Resolution
Authors: Carrell, H.L. / Rubin, B.H. / Hurley, T.J. / Glusker, J.P.
History
DepositionOct 11, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_database_status.process_site / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 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
Remark 700SHEET THE STRUCTURE OF THE MONOMER IS AN EIGHT-FOLD ALPHA-BETA BARREL WITH AN EXTENDED C-TERMINAL ...SHEET THE STRUCTURE OF THE MONOMER IS AN EIGHT-FOLD ALPHA-BETA BARREL WITH AN EXTENDED C-TERMINAL LOOP WHICH FACILITATES AGGREGATION OF MONOMERS TO TETRAMERS. TETRAMERS ARE POSITIONED ON THE 222 SYMMETRY SITE AT THE ORIGIN OF THE CELL.

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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)43,5144
Polymers43,2541
Non-polymers2603
Water5,242291
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)174,05716
Polymers173,0174
Non-polymers1,04012
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 area32550 Å2
ΔGint-166 kcal/mol
Surface area47050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.200, 100.200, 103.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: RESIDUE PRO 187 IS A CIS PROLINE.
Components on special symmetry positions
IDModelComponents
11A-484-

HOH

21A-656-

HOH

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Components

#1: Protein XYLOSE ISOMERASE


Mass: 43254.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Sugar ChemComp-XLS / D-xylose / D-XYLOSE (LINEAR FORM)


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE SUBSTRATE D-XYLOSE IS IN AN EXTENDED CONFORMATION AND APPEARS TO BE A MIXTURE OF D-XYLULOSE AND ...THE SUBSTRATE D-XYLOSE IS IN AN EXTENDED CONFORMATION AND APPEARS TO BE A MIXTURE OF D-XYLULOSE AND D-XYLOSE IN THE EXTENDED CONFORMATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal grow
*PLUS
pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mld-xylose isomerase1drop
20.76 M1reservoir(NH4)2SO4
30.01 MPIPES1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 38364 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.141

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→8 Å / σ(I): 1.5 /
RfactorNum. reflection
obs0.14 30656
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3044 0 12 291 3347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.044
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 30656 / σ(I): 1.5 / Rfactor obs: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS

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