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- PDB-1xib: MODES OF BINDING SUBSTRATES AND THEIR ANALOGUES TO THE ENZYME D-X... -

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Basic information

Entry
Database: PDB / ID: 1xib
TitleMODES OF BINDING SUBSTRATES AND THEIR ANALOGUES TO THE ENZYME D-XYLOSE ISOMERASE
ComponentsD-XYLOSE ISOMERASEXylose isomerase
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
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
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsCarrell, H.L. / Glusker, J.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Modes of binding substrates and their analogues to the enzyme D-xylose isomerase.
Authors: Carrell, H.L. / Hoier, H. / Glusker, J.P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: X-Ray Analysis of D-Xylose Isomerase at 1.9 Angstroms: Native Enzyme in Complex with Substrate and with a Mechanism-Designed Inactivator
Authors: Carrell, H.L. / Glusker, J.P. / Burger, V. / Manfre, F. / Biellmann, D.Tritsch J.-F.
#2: 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.
#3: 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
DepositionMar 7, 1994Processing site: BNL
SupersessionJun 22, 1994ID: 7XIA
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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Assembly

Deposited unit
A: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3643
Polymers43,2541
Non-polymers1102
Water6,810378
1
A: D-XYLOSE ISOMERASE
hetero molecules

A: D-XYLOSE ISOMERASE
hetero molecules

A: D-XYLOSE ISOMERASE
hetero molecules

A: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,45612
Polymers173,0174
Non-polymers4408
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 area31840 Å2
ΔGint-164 kcal/mol
Surface area46410 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
Atom site foot note1: CIS PROLINE - PRO 187
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

21A-660-

HOH

31A-712-

HOH

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Components

#1: Protein D-XYLOSE ISOMERASE / 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: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.78 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→9 Å / σ(I): 1.5 /
RfactorNum. reflection
obs0.152 46487
Refinement stepCycle: LAST / Resolution: 1.6→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 2 378 3431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d
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
Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.043

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