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- PDB-1a0c: XYLOSE ISOMERASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES -

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Basic information

Entry
Database: PDB / ID: 1a0c
TitleXYLOSE ISOMERASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES
ComponentsXYLOSE ISOMERASE
KeywordsKETOLISOMERASE / XYLOSE METABOLISM / GLUCOSE-FRUCTOSE INTERCONVERSION / HYDRIDE TRANSFER / ALPHA-BETA BARREL / METALLOENZYME / THERMOPHILE
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, bacterial-type / 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 speciesThermoanaerobacterium thermosulfurigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGallay, O. / Chopra, R. / Conti, E. / Brick, P. / Blow, D.
Citation
Journal: To be Published
Title: Crystal Structures of Class II Xylose Isomerases from Two Thermophiles and a Hyperthermophile
Authors: Gallay, O. / Chopra, R. / Conti, E. / Brick, P. / Jackson, R. / Hartley, B. / Vieille, C. / Zeikus, J.G. / Blow, D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Xylose Isomerase from Thermoanaerobacterium Thermosulfurigenes Strain 4B
Authors: Lloyd, L.F. / Gallay, O.S. / Akins, J. / Zeikus, J.G.
#2: Journal: Biochem.J. / Year: 1991
Title: Purification and Characterization of Thermostable Glucose Isomerase from Clostridium Thermosulfurogenes and Thermoanaerobacter Strain B6A
Authors: Lee, C.Y. / Zeikus, J.G.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: Catalytic Mechanism of Xylose (Glucose) Isomerase from Clostridium Thermosulfurogenes. Characterization of the Structural Gene and Function of Active Site Histidine
Authors: Lee, C.Y. / Bagdasarian, M. / Meng, M.H. / Zeikus, J.G.
History
DepositionNov 28, 1997Processing site: BNL
Revision 1.0Jun 3, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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_asym_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_asym_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLOSE ISOMERASE
B: XYLOSE ISOMERASE
C: XYLOSE ISOMERASE
D: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,11012
Polymers201,6394
Non-polymers4718
Water20,1051116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31970 Å2
ΔGint-242 kcal/mol
Surface area55520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.660, 153.730, 158.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.98821, 0.153, 0.00573), (0.15308, 0.98655, 0.05735), (0.00312, 0.05755, -0.99834)72.54202, -8.05105, 84.94467
2given(-0.75467, -0.00081, -0.65611), (0.00127, -1, -0.00024), (-0.65611, -0.00101, 0.75467)102.30876, 131.05106, 38.31144
3given(0.74332, -0.15209, 0.65141), (-0.1527, -0.98668, -0.05613), (0.65127, -0.05775, -0.75665)-8.31013, 139.06741, 54.78729

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Components

#1: Protein
XYLOSE ISOMERASE / GLUCOSE ISOMERASE


Mass: 50409.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium thermosulfurigenes (bacteria)
Strain: 4B / Cellular location: CYTOPLASM / Gene: XYLA / Plasmid: PCMG11 / Cellular location (production host): CYTOPLASM / Gene (production host): XYLA / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P19148, xylose isomerase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 2.6 Å3/Da / Density % sol: 48 %
Description: APPROXIMATE CELL DIMENSIONS A=85.9, B=154.0, C 159.0 WERE USED FOR SCALING AND MERGING; THE FINAL CELL DIMENSIONS WERE OBTAINED FROM POST-REFINEMENT.
Crystal growpH: 6
Details: PROTEIN IN 50 MM MOPS, 10 MM MGSO4, 1 MM COCL2, PH 7.0, WAS CRYSTALLIZED FROM 12% JEFFAMINE ED 4000, 50 MM MES, PH 6.0 (FOR DETAILS SEE REFERENCE 1).
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1993 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 61292 / % possible obs: 83.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.8 / % possible all: 73.6

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
IPMOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6XIA

6xia


Resolution: 2.5→10 Å / Rfactor Rfree error: 0.003 / Cross valid method: A POSTERIORI
Details: SOME DISORDERED SIDE CHAINS WERE NOT INCLUDED IN REFINEMENT. SOLVENT MOLECULES HOH 776, HOH 777, HOH 778 AND HOH 779 WERE NOT INCLUDED IN REFINEMENT SINCE THEY LIE ON OR NEAR TO NON- ...Details: SOME DISORDERED SIDE CHAINS WERE NOT INCLUDED IN REFINEMENT. SOLVENT MOLECULES HOH 776, HOH 777, HOH 778 AND HOH 779 WERE NOT INCLUDED IN REFINEMENT SINCE THEY LIE ON OR NEAR TO NON-CRYSTALLOGRAPHIC SYMMETRY AXES. SOLVENT MOLECULES WITH B > 60 A**2 WERE DELETED AFTER REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.177 3081 5 %RANDOM
Rwork0.168 ---
obs0.168 60986 84.9 %-
Displacement parametersBiso mean: 20.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 2 279 3785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.244 339 5 %
Rwork0.226 6334 -
obs--75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM.IONTOPH.ION

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