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- PDB-1a0d: XYLOSE ISOMERASE FROM BACILLUS STEAROTHERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1a0d
TitleXYLOSE ISOMERASE FROM BACILLUS STEAROTHERMOPHILUS
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 speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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: Biotechnol.Lett. / Year: 1993
Title: High Level Expression of a Thermostable Bacillus Xylose (Glucose) Isomerase in Escherichia Coli
Authors: Wuxiang, L. / Jeyaseelan, K.
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 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_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 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)200,73312
Polymers200,2944
Non-polymers4408
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29880 Å2
ΔGint-206 kcal/mol
Surface area54930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.290, 141.850, 160.660
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(-0.98767, 0.15658, -0.00024), (0.15655, 0.98752, 0.01744), (0.00296, 0.01718, -0.99985)28.20802, -2.89316, 78.8146
2given(-0.7424, -0.01277, -0.66983), (-0.01491, -0.99926, 0.03558), (-0.66979, 0.0364, 0.74166)55.16944, 50.51254, 20.18826
3given(0.72836, -0.14481, 0.66972), (-0.14472, -0.98787, -0.0562), (0.66974, -0.05599, -0.74048)-18.32721, 56.00223, 59.59824

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Components

#1: Protein
XYLOSE ISOMERASE / GLUCOSE ISOMERASE


Mass: 50073.395 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / Cellular location: CYTOPLASM / Strain: LLD-R / References: UniProt: P54273, xylose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOR DIFFUSION FROM HANGING DROPS (18 DEG C): PROTEIN (A280 22) WAS IN 50 MM TRIS, 10 MM MNCL2, PH 7.5; RESERVOIR SOLUTION WAS 10% PEG, 100 MM LICL, 100 MM MES, PH 6.3; DROPS WERE FORMED ...Details: VAPOR DIFFUSION FROM HANGING DROPS (18 DEG C): PROTEIN (A280 22) WAS IN 50 MM TRIS, 10 MM MNCL2, PH 7.5; RESERVOIR SOLUTION WAS 10% PEG, 100 MM LICL, 100 MM MES, PH 6.3; DROPS WERE FORMED FROM EQUAL PARTS OF PROTEIN AND RESERVOIR SOLUTIONS., pH 6.5, vapor diffusion - hanging drop
PH range: 6.3 - 7.5

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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: Feb 1, 1993 / Details: DUAL SLITS, COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→33 Å / Num. obs: 35985 / % possible obs: 89.6 % / Redundancy: 1.7 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.1 / % possible all: 62.2

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Processing

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

6xia


Resolution: 3→20 Å / Rfactor Rfree error: 0.005 / Cross valid method: A POSTERIORI
Details: OCCUPANCIES OF THE MN CATIONS AND WATER HOH 501 WERE REFINED, SIMULTANEOUSLY WITH TEMPERATURE FACTORS FOR ALL ATOMS, USING THE GROUP B COMMAND IN X-PLOR. THESE OCCUPANCIES WERE THEN FIXED AT ...Details: OCCUPANCIES OF THE MN CATIONS AND WATER HOH 501 WERE REFINED, SIMULTANEOUSLY WITH TEMPERATURE FACTORS FOR ALL ATOMS, USING THE GROUP B COMMAND IN X-PLOR. THESE OCCUPANCIES WERE THEN FIXED AT ROUNDED VALUES FOR THE SUBSEQUENT REFINEMENT PROTOCOL. DISORDERED SIDE CHAINS WERE NOT INCLUDED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1775 5 %RANDOM
Rwork0.193 ---
obs0.193 35802 89.3 %-
Displacement parametersBiso mean: 19.1 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 2 2 3485
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_d22.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
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: 3→3.14 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.282 124 5 %
Rwork0.303 2734 -
obs--57.9 %
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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