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- PDB-1s5m: Xylose Isomerase in Substrate and Inhibitor Michaelis States: Ato... -

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Basic information

Entry
Database: PDB / ID: 1s5m
TitleXylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift
ComponentsXylose isomerase
KeywordsISOMERASE / xylose isomerase / hydride shift / atomic resolution / tim barrel
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
alpha-D-glucopyranose / : / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces olivochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsFenn, T.D. / Ringe, D. / Petsko, G.A.
CitationJournal: Biochemistry / Year: 2004
Title: Xylose isomerase in substrate and inhibitor michaelis States: atomic resolution studies of a metal-mediated hydride shift(,).
Authors: Fenn, T.D. / Ringe, D. / Petsko, G.A.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_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_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _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 1.6Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 According to the author, the Swiss-Prot sequence (accession P15587)contains an error at position ... According to the author, the Swiss-Prot sequence (accession P15587)contains an error at position 175. Thr175 should be Ile175, however, the conflict is not yet noted in Swiss-Prot entry P15587.

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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)43,1936
Polymers42,8571
Non-polymers3365
Water7,404411
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)172,77224
Polymers171,4284
Non-polymers1,34420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area33790 Å2
ΔGint-263 kcal/mol
Surface area44910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.865, 92.968, 98.298
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-2142-

HOH

21A-2253-

HOH

31A-2333-

HOH

41A-2368-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 42856.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces olivochromogenes (bacteria)
Gene: XYLA / Plasmid: pX15 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P15587, xylose isomerase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.15 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.1M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 398K
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlxylose isomerase1drop
250 mMHEPES1droppH7.5
310 mM1dropMnCl2
42.1-2.35 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
211
ReflectionResolution: 0.98→50 Å / Num. all: 229134 / Num. obs: 212189 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.1
Reflection shellResolution: 0.98→1.02 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.3 / % possible all: 83.4
Reflection shell
*PLUS
% possible obs: 83.4 % / Num. unique obs: 20308

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STREPTOMYCES OLIVOCHROMOGENES XYLOSE ISOMERASE - PDB ID 1XYA

1xya


Resolution: 0.98→50 Å / Num. parameters: 33226 / Num. restraintsaints: 43898 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.3%
RfactorNum. reflection% reflectionSelection details
Rfree0.1293 10601 5 %RANDOM
Rwork0.1109 ---
all0.1111 212189 --
obs-212189 94.9 %-
Refine analyzeNum. disordered residues: 58 / Occupancy sum hydrogen: 2924.75 / Occupancy sum non hydrogen: 3448.32
Refinement stepCycle: LAST / Resolution: 0.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 16 411 3452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.095
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.105
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.026
X-RAY DIFFRACTIONs_chiral_restr0.101

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