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- PDB-1a0e: XYLOSE ISOMERASE FROM THERMOTOGA NEAPOLITANA -

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Basic information

Entry
Database: PDB / ID: 1a0e
TitleXYLOSE ISOMERASE FROM THERMOTOGA NEAPOLITANA
ComponentsXYLOSE ISOMERASE
KeywordsKETOLISOMERASE / XYLOSE METABOLISM / GLUCOSE-FRUCTOSE INTERCONVERSION / HYDRIDE TRANSFER / ALPHA-BETA BARREL / METALLOENZYME / THERMOPHILE
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / 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 speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Initial X-Ray Analysis of Xylose Isomerase from Thermotoga Neapolitana
Authors: Chayen, N.E. / Conti, E. / Vieille, C. / Zeikus, J.G.
#2: Journal: Appl.Environ.Microbiol. / Year: 1995
Title: Xyla Cloning and Sequencing and Biochemical Characterization of Xylose Isomerase from Thermotoga Neapolitana
Authors: Vieille, C. / Hess, J.M. / Kelly, R.M. / 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: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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_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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Advisory / Derived calculations / Refinement description
Category: pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,0178
Polymers101,6632
Non-polymers3546
Water4,612256
1
A: XYLOSE ISOMERASE
D: XYLOSE ISOMERASE
hetero molecules

A: XYLOSE ISOMERASE
D: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,03416
Polymers203,3264
Non-polymers70712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area30610 Å2
ΔGint-287 kcal/mol
Surface area55690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)161.790, 121.870, 98.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-493-

CO

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99999, 0.00298, 0.0021), (-0.00259, -0.98577, 0.16811), (0.00257, 0.1681, 0.98577)
Vector: 80.53531, 0.16098, -0.04196)

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Components

#1: Protein XYLOSE ISOMERASE / / GLUCOSE ISOMERASE


Mass: 50831.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Strain: 5068 / Cellular location: CYTOPLASM / Gene: XYLA / Plasmid: PTNE2 / Cellular location (production host): CYTOPLASM / Gene (production host): XYLA / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P45687, xylose isomerase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 14% JEFFAMINE ED 4000, 5 MM MGSO4, 0.5 MM COCL2, 50 MM MOPS, PH 7.0 (FOR DETAILS SEE REFERENCE 1).

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 1, 1994 / Details: DUAL SLIT, COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→12.5 Å / Num. obs: 26137 / % possible obs: 96.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.88 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 4.3 / % possible all: 93.9

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: XYLOSE ISOMERASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES

Resolution: 2.7→12.5 Å / Rfactor Rfree error: 0.006 / Cross valid method: A POSTERIORI
Details: DISORDERED SIDE CHAINS WERE NOT INCLUDED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1265 5 %RANDOM
Rwork0.18 ---
obs0.18 26119 97.1 %-
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 6 256 7274
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
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: 2.7→2.82 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.313 144 5 %
Rwork0.288 2957 -
obs--93.1 %
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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