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- PDB-1gw9: Tri-iodide derivative of Xylose Isomerase from Streptomyces Rubig... -

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Basic information

Entry
Database: PDB / ID: 1gw9
TitleTri-iodide derivative of Xylose Isomerase from Streptomyces Rubiginosus
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE / PENTOSE SHUNT / XYLOSE METABOLISM / MAGNESIUM
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
IODIDE ION / beta-L-xylopyranose / Xylose isomerase
Similarity search - Component
Biological speciesSTREPTOMYCES RUBIGINOSUS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.55 Å
AuthorsEvans, G. / Bricogne, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods for Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment
Authors: Evans, G. / Bricogne, G.
History
DepositionMar 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 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: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,31534
Polymers43,2541
Non-polymers4,06133
Water6,251347
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)189,259136
Polymers173,0174
Non-polymers16,243132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.354, 98.540, 102.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2250-

HOH

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Components

#1: Protein XYLOSE ISOMERASE


Mass: 43254.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES RUBIGINOSUS (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-LXC / beta-L-xylopyranose / beta-L-xylose / L-xylose / xylose / L-XYLOSE (CYCLIC FORM)


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-xylopyranoseCOMMON NAMEGMML 1.0
b-L-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5
Details: 1.8M AMMONIUM SULPHATE, 10MM TRIS-HCL AT PH7.5 AND THEN SOAKED IN AN EQUIVALENT SOLUTION WITH 50MM KI/50MM I2 AND 1.9M L-XYLOSE ADDED AS CRYO-PROTECTANT., pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
20.9 Mammonium sulfate1drop
310 mMTris-HCl1droppH7.5
41.8 Mammonium sulfate1reservoir
510 mMTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: OSMIC MULTILAYER
RadiationMonochromator: OSMIC MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→32.05 Å / Num. obs: 1257016 / % possible obs: 98.6 % / Observed criterion σ(I): 6 / Redundancy: 18.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.4
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 13 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.7 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 32.11 Å
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameClassification
BUSTER-TNTrefinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.55→32.05 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3400 5 %RANDOM
Rwork0.164 ---
obs0.165 66821 98.6 %-
Refinement stepCycle: LAST / Resolution: 1.55→32.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 51 347 3419
Refinement
*PLUS
Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1.619

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