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- PDB-3hee: Structural study of Clostridium thermocellum Ribose-5-Phosphate I... -

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Basic information

Entry
Database: PDB / ID: 3hee
TitleStructural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B and ribose-5-phosphate
ComponentsRibose-5-phosphate isomerase
KeywordsISOMERASE / D-Ribose Phosphate Isomerase / ctRpi B / Isomerization / Ribose-5- Phosphate
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
RIBOSE-5-PHOSPHATE / Sugar-phosphate isomerase, RpiB/LacA/LacB family
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKang, L.W. / Kim, J.K. / Jung, J.H. / Hong, M.K.
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
DepositionMay 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: 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_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

Downloads & links

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Assembly

Deposited unit
A: Ribose-5-phosphate isomerase
B: Ribose-5-phosphate isomerase
B: RIBOSE-5-PHOSPHATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7634
Polymers32,3032
Non-polymers4602
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-19 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.381, 69.381, 153.566
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-200-

HOH

21A-228-

HOH

31B-194-

HOH

41B-216-

HOH

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Components

#1: Protein Ribose-5-phosphate isomerase


Mass: 16151.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cthe_2597 / Plasmid: pET 28a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A3DIL8, ribose-5-phosphate isomerase
#2: Sugar ChemComp-R5P / RIBOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M Tris, pH7.0, 10% PEG8000, 0.15M Magnesium chloride, 0.2M Potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29281 / % possible obs: 98.3 % / Observed criterion σ(F): 1.3 / Observed criterion σ(I): 1.2 / Redundancy: 16.3 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 31.6
Reflection shellResolution: 2→50 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 31.6 / Num. unique all: 29281 / Rsym value: 0.095 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
swiss-modelmodel building
REFMAC5.2.0019refinement
swiss-modelphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVR

2vvr


Resolution: 2→33.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.083 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22051 1487 5.1 %RANDOM
Rwork0.17433 ---
obs0.17668 27713 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.078 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 28 165 2437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222302
X-RAY DIFFRACTIONr_angle_refined_deg2.1921.973090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28123.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51115408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4381518
X-RAY DIFFRACTIONr_chiral_restr0.1740.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021702
X-RAY DIFFRACTIONr_nbd_refined0.2150.21170
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21592
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2166
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4350.213
X-RAY DIFFRACTIONr_mcbond_it1.621.51516
X-RAY DIFFRACTIONr_mcangle_it2.24122286
X-RAY DIFFRACTIONr_scbond_it4.1133926
X-RAY DIFFRACTIONr_scangle_it5.8774.5804
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 88 -
Rwork0.228 1677 -
obs--81.49 %

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