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- PDB-4xis: A METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BAS... -

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Basic information

Entry
Database: PDB / ID: 4xis
TitleA METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BASED ON THE 1.6 ANGSTROMS STREPTOMYCES RUBIGINOSUS STRUCTURES WITH XYLITOL AND D-XYLOSE
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / 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
: / D-xylose / alpha-D-xylopyranose / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsWhitlow, M. / Howard, A.J.
CitationJournal: Proteins / Year: 1991
Title: A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose.
Authors: Whitlow, M. / Howard, A.J. / Finzel, B.C. / Poulos, T.L. / Winborne, E. / Gilliland, G.L.
History
DepositionMar 25, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / refine / struct_conn / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _chem_comp.name ..._atom_site.label_alt_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_validate_chiral.label_alt_id / _refine.pdbx_ls_sigma_I
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 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 SHEET S1 IS ACTUALLY AN EIGHT-STRANDED BETA BARREL. THIS IS REPRESENTED BY A NINE-STRANDED ...SHEET SHEET S1 IS ACTUALLY AN EIGHT-STRANDED BETA BARREL. THIS 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: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5625
Polymers43,1521
Non-polymers4104
Water7,206400
1
A: XYLOSE ISOMERASE
hetero molecules

A: XYLOSE ISOMERASE
hetero molecules

A: XYLOSE ISOMERASE
hetero molecules

A: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,24920
Polymers172,6084
Non-polymers1,64116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area34620 Å2
ΔGint-152 kcal/mol
Surface area46060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.640, 99.970, 103.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: RESIDUE 187 IS A CIS PROLINE.

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Components

#1: Protein XYLOSE ISOMERASE


Mass: 43152.105 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: Sugar ChemComp-XLS / D-xylose / D-XYLOSE (LINEAR FORM)


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#3: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: obtained synthetically / 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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.0 mg/mlenzyme1drop
221 %satammonium sulfate1drop
30.5 mM1dropMgCl2
450 mMHEPES1drop
543 %satammonium sulfate1reservoir
650 mMHEPES1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.53 Å / Num. obs: 70624 / % possible obs: 98 % / Num. measured all: 379659

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→10 Å /
RfactorNum. reflection
obs0.135 58447
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 22 400 3455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.031
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: PLOLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Num. reflection all: 70624 / Num. reflection obs: 58447 / σ(I): 2 / Rfactor obs: 0.135
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_planar_d0.045
X-RAY DIFFRACTIONx_plane_restr4.5

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