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- PDB-9xia: X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZ... -

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Basic information

Entry
Database: PDB / ID: 9xia
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
3-deoxy-3-methyl-beta-D-fructofuranose / : / 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 2.0Jul 29, 2020Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
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)43,5424
Polymers43,2541
Non-polymers2883
Water5,386299
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)174,16916
Polymers173,0174
Non-polymers1,15212
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 area33330 Å2
ΔGint-161 kcal/mol
Surface area46170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.800, 100.000, 103.000
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-483-

HOH

21A-649-

HOH

DetailsTHE 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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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-DFR / 3-deoxy-3-methyl-beta-D-fructofuranose / 3-DEOXY-3-METHYL-D-FRUCTOSE / 3-deoxy-3-methyl-beta-D-fructose / 3-deoxy-3-methyl-fructose


Type: D-saccharide, beta linking / Mass: 178.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
#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.: 299 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AMINO ACID SEQUENCE WAS TAKEN FROM INTERNATIONAL PATENT APPLICATION NUMBER:PCT/US88/02765, ...THE AMINO ACID SEQUENCE WAS TAKEN FROM INTERNATIONAL PATENT APPLICATION NUMBER:PCT/US88/02765, INTERNATIONAL PUBLICATION NUMBER:WO89/01520. IN THIS PATENT RESIDUE 41 IS SPECIFIED AS ARG. HOWEVER, RESIDUE 41 APPEARS TO BE GLN BASED ON THE CRYSTALLOGRAPHIC STUDY. IN THIS ENTRY RESIDUE 41 IS PRESENTED AS GLN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein11
20.76 Mammonium sulfate11
30.01 MPIPES11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 36274 / % possible obs: 94 % / Num. measured all: 71368 / Biso Wilson estimate: 22 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→8 Å /
RfactorNum. reflection
obs0.141 30250
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 14 299 3360
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.023
X-RAY DIFFRACTIONp_angle_d0.045
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
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 30250 / σ(I): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17 Å2

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