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- PDB-4xia: STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 C... -

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Basic information

Entry
Database: PDB / ID: 4xia
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 / D-xylose metabolic process / xylose isomerase activity / 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
sorbitol / Xylose isomerase
Similarity search - Component
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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 1.5Feb 28, 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)86,3096
Polymers85,8962
Non-polymers4134
Water9,692538
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)172,61712
Polymers171,7914
Non-polymers8268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area34000 Å2
ΔGint-175 kcal/mol
Surface area44350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.800, 105.800, 153.400
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 158 DEVIATES SIGNIFICANTLY FROM THE EXPECTED VALUE AND IS LIKELY TO BE INCORRECT.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8839, -0.0648, 0.4632), (-0.0706, -0.9605, -0.269), (0.4624, -0.2705, 0.8444)
Vector: 66.28, 115.1, 0.16)

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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-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O6
#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.: 538 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
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: 2.3 Å / Num. obs: 44186 / % possible obs: 98.8 % / Num. measured all: 127622 / Rmerge(I) obs: 0.062

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→6 Å
Details: THE CD-NE-CZ ANGLE OF ARG A 158 DEVIATES SIGNIFICANTLY FROM THE EXPECTED VALUE AND IS LIKELY TO BE INCORRECT.
RfactorNum. reflection
obs0.147 41617
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 26 538 6618
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.025
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.911.5
X-RAY DIFFRACTIONp_mcangle_it1.462
X-RAY DIFFRACTIONp_scbond_it1.952
X-RAY DIFFRACTIONp_scangle_it2.983
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.150.15
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_tor15.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. reflection obs: 43615 / Rfactor obs: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS

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