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- PDB-3ph3: Clostridium thermocellum Ribose-5-Phosphate Isomerase B with d-ribose -

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Basic information

Entry
Database: PDB / ID: 3ph3
TitleClostridium thermocellum Ribose-5-Phosphate Isomerase B with d-ribose
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-ribose / 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 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 1, 2020Group: Atomic model / Data collection / Database references
Category: atom_site / pdbx_validate_chiral / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)36,9464
Polymers36,6462
Non-polymers3002
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-18 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.033, 69.033, 154.583
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-168-

HOH

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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, ribose-5-phosphate isomerase
#2: Sugar ChemComp-RB5 / D-ribose


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 57.61 %
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: 26917 / Num. obs: 26917 / % possible obs: 100 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2
Reflection shellResolution: 2.1→2.2 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE8

3he8


Resolution: 2.07→39.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.328 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23758 1284 5 %RANDOM
Rwork0.19937 ---
obs0.20128 24355 95.79 %-
all-24355 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.101 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.07→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 20 149 2413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222294
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9663076
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38123.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2615408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8491518
X-RAY DIFFRACTIONr_chiral_restr0.1410.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021702
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_it1.1581.51442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0422286
X-RAY DIFFRACTIONr_scbond_it3.7093852
X-RAY DIFFRACTIONr_scangle_it5.6614.5790
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
Rfree0.344 88 -
Rwork0.298 1838 -
obs--99.38 %

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