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- PDB-2glk: High-resolution study of D-Xylose isomerase, 0.94A resolution. -

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Basic information

Entry
Database: PDB / ID: 2glk
TitleHigh-resolution study of D-Xylose isomerase, 0.94A resolution.
ComponentsXylose isomerase
KeywordsISOMERASE / TIM barrel / beta-alpha-barrels / two metal binding sites
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
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsKatz, A.K. / Carrell, H.L. / Hanson, B.L. / Harp, J.M. / Glusker, J.P. / Bunick, G.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction.
Authors: Katz, A.K. / Li, X. / Carrell, H.L. / Hanson, B.L. / Langan, P. / Coates, L. / Schoenborn, B.P. / Glusker, J.P. / Bunick, G.J.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,7627
Polymers43,2831
Non-polymers4786
Water7,674426
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)175,04628
Polymers173,1334
Non-polymers1,91324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area36600 Å2
ΔGint-180 kcal/mol
Surface area45550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.712, 97.935, 101.867
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-1147-

HOH

Detailshomo-tetramer consisting of subunits related by crystallographic 222 symmetry.

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 50mM tris-HCl,25%AMSO4,2mM Mn2+ and 2mM Co2+ , XI @ 25mg/ml., pH 8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.94→35.36 Å / Num. all: 252079 / Num. obs: 252079 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 0.944→0.965 Å / % possible all: 12

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
X-GENdata reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XIB

1xib


Resolution: 0.94→35.36 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.304 / SU ML: 0.008 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12792 21042 8.3 %RANDOM
Rwork0.11458 ---
all0.1157 252079 --
obs0.1157 231037 85.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.123 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 0.94→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 26 426 3506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213263
X-RAY DIFFRACTIONr_bond_other_d0.0020.022939
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9574406
X-RAY DIFFRACTIONr_angle_other_deg1.86936801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82422.903186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41415534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7871541
X-RAY DIFFRACTIONr_chiral_restr0.1120.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023717
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02746
X-RAY DIFFRACTIONr_nbd_refined0.2350.2722
X-RAY DIFFRACTIONr_nbd_other0.2050.22970
X-RAY DIFFRACTIONr_nbtor_refined0.190.21627
X-RAY DIFFRACTIONr_nbtor_other0.0950.21679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.340.2198
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.232
X-RAY DIFFRACTIONr_mcbond_it2.1181.52506
X-RAY DIFFRACTIONr_mcbond_other1.3161.5806
X-RAY DIFFRACTIONr_mcangle_it2.5623112
X-RAY DIFFRACTIONr_scbond_it3.43631520
X-RAY DIFFRACTIONr_scangle_it4.6954.51294
X-RAY DIFFRACTIONr_rigid_bond_restr1.84233805
X-RAY DIFFRACTIONr_sphericity_free11.8673429
X-RAY DIFFRACTIONr_sphericity_bonded5.91433031
LS refinement shellResolution: 0.944→0.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 252 -
Rwork0.41 2829 -
obs--14.24 %

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