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- PDB-2xim: ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS -

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Basic information

Entry
Database: PDB / ID: 2xim
TitleARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS
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 speciesActinoplanes missouriensis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMrabet, N.T. / Van Denbroek, A. / Van Den Brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.-M. / Matthyssens, G. / Jenkins, J. / Chiadmi, M. / Vantilbeurgh, H. ...Mrabet, N.T. / Van Denbroek, A. / Van Den Brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.-M. / Matthyssens, G. / Jenkins, J. / Chiadmi, M. / Vantilbeurgh, H. / Rey, F. / Janin, J. / Quax, W.J. / Lasters, I. / Demaeyer, M. / Wodak, S.J.
Citation
Journal: Biochemistry / Year: 1992
Title: Arginine residues as stabilizing elements in proteins.
Authors: Mrabet, N.T. / Van den Broeck, A. / Van den brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.M. / Matthijssens, G. / Jenkins, J. / Chiadmi, M. / van Tilbeurgh, H. / Rey, F. / Janin, J. ...Authors: Mrabet, N.T. / Van den Broeck, A. / Van den brande, I. / Stanssens, P. / Laroche, Y. / Lambeir, A.M. / Matthijssens, G. / Jenkins, J. / Chiadmi, M. / van Tilbeurgh, H. / Rey, F. / Janin, J. / Quax, W.J. / Lasters, I. / Demaeyer, M. / Wodak, S.J.
#1: 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
DepositionMay 29, 1991Processing site: BNL
Revision 1.0Apr 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 / _chem_comp.type ..._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.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 21, 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)174,60116
Polymers173,7984
Non-polymers80312
Water16,556919
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34360 Å2
ΔGint-190 kcal/mol
Surface area46520 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.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8028, 0.5757, -0.1552), (0.5753, 0.6797, -0.455), (-0.1564, -0.4546, -0.8769)40.88, 83.55, 360.39999
2given(0.648, -0.6645, -0.3721), (-0.6648, -0.7319, 0.1493), (-0.3716, 0.1507, -0.9161)116.73, 102.09, 334.95999
3given(-0.8443, 0.0901, 0.5282), (0.0889, -0.9485, 0.304), (0.5284, 0.3036, 0.7929)-46.4, 67.8, 2.17

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Components

#1: Protein
D-XYLOSE ISOMERASE


Mass: 43449.523 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-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H12O5
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LYS 253 TO ARG MUTATION YIELDS A THERMOSTABLE ENZYME WITH WILD TYPE ACTIVITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.9 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
20.1 Msodium phosphate1drop
31 Mammonium sulfate1drop
41.2 Mammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 108522 / Num. measured all: 240939 / Rmerge(I) obs: 0.073

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2.3 Å /
RfactorNum. reflection
obs0.149 108519
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12220 0 48 919 13187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.038
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.037
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_restr0.009
X-RAY DIFFRACTIONp_chiral_restr0.128
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd0.267
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.2 Å2

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