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- PDB-1muw: The 0.86 Angstrom Structure of Xylose Isomerase -

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Basic information

Entry
Database: PDB / ID: 1muw
TitleThe 0.86 Angstrom Structure of Xylose Isomerase
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE / xylose isomerase / atomic resolution / disorder
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
: / HYDROXIDE ION / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces olivochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 Å
AuthorsFenn, T.D. / Ringe, D. / Petsko, G.A.
CitationJournal: To be Published
Title: Active Site Dynamics at 0.86A: Crystallographic Analysis of a Metal-Mediated Hydride Shift
Authors: Fenn, T.D. / Ringe, D. / Petsko, G.A.
History
DepositionSep 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_alt_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.pdbx_ptnr2_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Author states the seqres is not available in the database, as it was never deposited by ...SEQUENCE Author states the seqres is not available in the database, as it was never deposited by the authors at the time. The reference to the corrected sequence is Gerhardt, E. (1993) Gezielte Mutagenese Eines Histidinrestes im Aktiven Zentrum der D-Xylose Isomerase von Streptomyces olivochromogenes: Biochemische und Strukturelle Analyse der Mutante. Ph.D. dissertation, University of Heidelberg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0326
Polymers42,8571
Non-polymers1755
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)172,13024
Polymers171,4284
Non-polymers70220
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 area32330 Å2
ΔGint-267 kcal/mol
Surface area45680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.906, 92.883, 98.321
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-593-

HOH

21A-713-

HOH

31A-862-

HOH

41A-872-

HOH

51A-899-

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)
Plasmid: PX15 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P15587, xylose isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM MgCl2, 2.2M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.918 / Wavelength: 0.918 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 3, 2002 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 0.8→50 Å / Num. all: 358727 / Num. obs: 358727 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.8
Reflection shellResolution: 0.8→0.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.8 / Num. unique all: 37312 / % possible all: 92

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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: PDB ENTRY 1XYA

1xya


Resolution: 0.86→50 Å / Num. parameters: 35246 / Num. restraintsaints: 49011 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1431 17954 5 %RANDOM
Rwork0.1244 ---
all0.1255 358727 --
obs0.1255 358727 100 %-
Refine analyzeNum. disordered residues: 88 / Occupancy sum hydrogen: 2913.39 / Occupancy sum non hydrogen: 3477.06
Refinement stepCycle: LAST / Resolution: 0.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 5 449 3479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0271
X-RAY DIFFRACTIONs_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.116

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