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- PDB-8xim: PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLAN... -

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Basic information

Entry
Database: PDB / ID: 8xim
TitlePROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES
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
D-xylose / Xylose isomerase
Similarity search - Component
Biological speciesActinoplanes missouriensis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsJanin, J.
Citation
Journal: Biochemistry / Year: 1992
Title: Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites.
Authors: Jenkins, J. / Janin, J. / Rey, F. / Chiadmi, M. / van Tilbeurgh, H. / Lasters, I. / De Maeyer, M. / Van Belle, D. / Wodak, S.J. / Lauwereys, M. / Stanssens, P. / Matthyssens, G. / Lambeir, A.M.
#1: Journal: Biochemistry / Year: 1992
Title: Protein Engineering of Xylose (Glucose) Isomerase from Actinoplanes Missouriensis. 2. Site-Directed Mutagenesis of the Xylose Binding Site
Authors: Lambeir, A.-M. / Lauwereys, M. / Stanssens, P. / Mrabet, N.T. / Snauwaert, J. / Vantilbeurgh, H. / Matthyssens, G. / Lasters, I. / Demaeyer, M. / Wodak, S.J. / Jenkins, J. / Chiadmi, M. / Janin, J.
#2: Journal: Biochemistry / Year: 1992
Title: Protein Engineering of Xylose (Glucose) Isomerase from Actinoplanes Missouriensis. 3. Changing Metal Specificity and the Ph Profile by Site-Directed Mutagenesis
Authors: Vantilbeurgh, H. / Jenkins, J. / Chiadmi, M. / Wodak, J.Janin S.J. / Mrabet, N.T. / Lambeir, A.-M.
#3: Journal: Biochemistry / Year: 1992
Title: Arginine Residues as Stabilizing Elements in Proteins
Authors: Mrabet, N.T. / Van Denbroek, A. / Van Den Brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.-M. / Matthijssens, G. / Jenkins, J. / Chiadmi, M. / Vantilbeurgh, H. / Rey, F. / Janin, J. / ...Authors: Mrabet, N.T. / Van Denbroek, A. / Van Den Brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.-M. / Matthijssens, G. / Jenkins, J. / Chiadmi, M. / Vantilbeurgh, H. / Rey, F. / Janin, J. / Quax, W.J. / Lasters, I. / Demaeyer, M. / Wodak, S.J.
#4: Journal: Proteins / Year: 1988
Title: Structural Analysis of the 2.8 Angstroms Model of Xylose Isomerase from Actinoplanes Missouriensis
Authors: Rey, F. / Jenkins, J. / Janin, J. / Lasters, I. / Alard, P. / Claessens, M. / Matthyssens, G. / Wodak, S.
History
DepositionApr 1, 1992Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / 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.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

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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
C: D-XYLOSE ISOMERASE
D: D-XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,38012
Polymers173,6824
Non-polymers6988
Water17,493971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33700 Å2
ΔGint-150 kcal/mol
Surface area46590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.450, 143.450, 231.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUES PRO A 187, PRO B 187, PRO C 187, AND PRO D 187 ARE CIS PROLINES.

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Components

#1: Protein
D-XYLOSE ISOMERASE


Mass: 43420.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes missouriensis (bacteria) / References: UniProt: P12851, xylose isomerase
#2: Sugar
ChemComp-XLS / D-xylose / D-XYLOSE (LINEAR FORM)


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 971 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMG 395 IS AT METAL SITE 1 IN ALL FOUR SUBUNITS. THE MG AT METAL SITE 2 HAS BEEN REPLACED WITH WATER ...MG 395 IS AT METAL SITE 1 IN ALL FOUR SUBUNITS. THE MG AT METAL SITE 2 HAS BEEN REPLACED WITH WATER HOH 396 IN ALL FOUR SUBUNITS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.92 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
21 Mammonium sulfate1drop
30.1 Msodium phosphate1drop
41.2 Mammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 97974 / Rmerge(I) obs: 0.063 / Num. measured all: 244294

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2.4 Å /
RfactorNum. reflection
obs0.146 97974
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12188 0 44 971 13203
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.04
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_restr0.0090.01
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd0.2650.5
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: 2.4 Å / Num. reflection obs: 97974 / Rfactor obs: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.8 Å2

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