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- PDB-3ph4: Clostridium thermocellum Ribose-5-Phosphate Isomerase B with d-allose -

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Basic information

Entry
Database: PDB / ID: 3ph4
TitleClostridium thermocellum Ribose-5-Phosphate Isomerase B with d-allose
ComponentsRibose-5-phosphate isomerase
KeywordsISOMERASE / alpha-beta-alpha sandwich fold
Function / homology
Function and homology information


ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / carbohydrate metabolic process
Similarity search - Function
: / Ribose 5-phosphate isomerase B / Sugar-phosphate isomerase, RpiB/LacA/LacB family / Sugar-phosphate isomerase, RpiB/LacA/LacB superfamily / Ribose/Galactose Isomerase / Ribose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-ALLOSE / Sugar-phosphate isomerase, RpiB/LacA/LacB family
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsJung, J. / Kim, J.-K. / Yeom, S.-J. / Ahn, Y.-J. / Oh, D.-K. / Kang, L.-W.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2011
Title: Crystal structure of Clostridium thermocellum ribose-5-phosphate isomerase B reveals properties critical for fast enzyme kinetics.
Authors: Jung, J. / Kim, J.K. / Yeom, S.J. / Ahn, Y.J. / Oh, D.K. / Kang, L.W.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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 / _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: Ribose-5-phosphate isomerase
B: Ribose-5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0064
Polymers36,6462
Non-polymers3602
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-19 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.134, 69.134, 154.284
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ribose-5-phosphate isomerase


Mass: 18322.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_2597 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DIL8
#2: Sugar ChemComp-AOS / D-ALLOSE


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M Tris pH 7.0, 10% PEG 8000, 0.15M Magnesium chloride, 0.2M Potassium chloride , VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.24 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 17, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 25673 / Num. obs: 25673 / % possible obs: 95.7 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2
Reflection shellResolution: 2.1→2.2 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE8

3he8


Resolution: 2.07→39.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.585 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22004 1333 5 %RANDOM
Rwork0.1842 ---
all0.18599 25106 --
obs0.18599 25106 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.07→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 24 176 2444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.9653082
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6623.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8511518
X-RAY DIFFRACTIONr_chiral_restr0.160.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021702
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1941.51442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08222286
X-RAY DIFFRACTIONr_scbond_it3.6973856
X-RAY DIFFRACTIONr_scangle_it5.6624.5796
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 99 -
Rwork0.251 1839 -
obs--100 %

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