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- PDB-5xia: STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 C... -

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Basic information

Entry
Database: PDB / ID: 5xia
TitleSTRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY
ComponentsD-XYLOSE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion 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
Xylitol / Xylose isomerase
Similarity search - Component
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHenrick, K. / Collyer, C.A. / Blow, D.M.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively.
Authors: Henrick, K. / Collyer, C.A. / Blow, D.M.
#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: Biochim.Biophys.Acta / Year: 1986
Title: The Crystallization of Glucose Isomerase from Arthrobacter B3728
Authors: Akins, J. / Brick, P. / Jones, H.B. / Hirayama, N. / Shaw, P.-C. / Blow, D.M.
History
DepositionJul 5, 1989Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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 1.5Mar 13, 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 TWO SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT- ...SHEET THE TWO SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. EACH IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2496
Polymers85,8962
Non-polymers3534
Water10,359575
1
A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules

A: D-XYLOSE ISOMERASE
B: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,49712
Polymers171,7914
Non-polymers7068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area33890 Å2
ΔGint-180 kcal/mol
Surface area44830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.900, 105.900, 153.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: RESIDUES PRO A 186 AND PRO B 186 ARE CIS PROLINES.
2: THE CD-NE-CZ ANGLE OF ARG A 289 DEVIATES SIGNIFICANTLY FROM THE EXPECTED VALUE AND IS LIKELY TO BE INCORRECT.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8882, -0.06204, 0.45405), (-0.06744, -0.9623, -0.26351), (0.45327, -0.26483, 0.85112)
Vector: 66.43, 115.38, 0.13)

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Components

#1: Protein D-XYLOSE ISOMERASE


Mass: 42947.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: NRRL B3728 / References: UniProt: P12070, xylose isomerase
#2: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE ARE MAJOR DISCREPANCIES BETWEEN THIS MODEL OF XYLOSE ISOMERASE AND THAT PRESENTED IN PROTEIN ...THERE ARE MAJOR DISCREPANCIES BETWEEN THIS MODEL OF XYLOSE ISOMERASE AND THAT PRESENTED IN PROTEIN DATA BANK ENTRY 3XIA (G.K.FARBER ET AL., BIOCHEMISTRY, V. 28, P. 7289 (1989)). THE ALMOST IDENTICAL STRUCTURES OF ARTHROBACTER AND STREPTOMYCES RUBIGINOSUS XYLOSE ISOMERASES (K.HENRICK ET AL., PROTEIN. ENG., V. 1, P. 467 (1987)) AND SEQUENCE HOMOLOGIES SUGGEST THAT 3XIA SHOULD BE STRUCTURALLY EQUIVALENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: Akins, J., (1986) Biochim.Biophys.Acta, 874, 375.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlprotein1drop
21.2 Mammonium sulfate1drop
350 mMTris-acetate1reservoir
410 mM1reservoirMgCl2

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 33532 / % possible obs: 95.5 % / Num. measured all: 73748 / Rmerge(I) obs: 0.044

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.5→6 Å
Details: THE CD-NE-CZ ANGLE OF ARG A 289 DEVIATES SIGNIFICANTLY FROM THE EXPECTED VALUE AND IS LIKELY TO BE INCORRECT.
RfactorNum. reflection
obs0.135 31019
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 22 575 6651
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.025
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.941.5
X-RAY DIFFRACTIONp_mcangle_it1.542
X-RAY DIFFRACTIONp_scbond_it1.932
X-RAY DIFFRACTIONp_scangle_it2.983
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.160.2
X-RAY DIFFRACTIONp_multtor_nbd0.220.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor17.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / Num. reflection obs: 32989 / Rfactor obs: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS

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