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- PDB-3uxi: Crystal structure of L-rhamnose isomerase W38A mutant from Bacill... -

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Basic information

Entry
Database: PDB / ID: 3uxi
TitleCrystal structure of L-rhamnose isomerase W38A mutant from Bacillus halodurans
ComponentsL-Rhamnose isomerase
KeywordsISOMERASE / (beta/alpha)8 barrel domain
Function / homology
Function and homology information


L-rhamnose isomerase / L-rhamnose isomerase activity / L-lyxose metabolic process / rhamnose catabolic process / manganese ion binding / cytoplasm
Similarity search - Function
Rhamnose isomerase / L-rhamnose isomerase (RhaA) / : / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / L-rhamnose isomerase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsDoan, T.T.N. / Prabhu, P. / Kim, J.K. / Jeya, M. / Kang, L.W. / Lee, J.K.
CitationJournal: Febs J. / Year: 2014
Title: Structure-based studies on the metal binding of two-metal-dependent sugar isomerases.
Authors: Prabhu, P. / Doan, T.N. / Tiwari, M. / Singh, R. / Kim, S.C. / Hong, M.K. / Kang, Y.C. / Kang, L.W. / Lee, J.K.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: L-Rhamnose isomerase
B: L-Rhamnose isomerase
C: L-Rhamnose isomerase
D: L-Rhamnose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,8975
Polymers195,8424
Non-polymers551
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20450 Å2
ΔGint-62 kcal/mol
Surface area55470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.380, 164.794, 92.837
Angle α, β, γ (deg.)90.00, 117.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-Rhamnose isomerase


Mass: 48960.570 Da / Num. of mol.: 4 / Mutation: W38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: rhaA, BH1552 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KCL9, L-rhamnose isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 57.6 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 6.5
Details: 10% (w/v) PEG 8000, 0.1M HEPES pH 6.0, 0.2M sodium acetate, VAPOR DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 90338 / % possible obs: 79 %
Reflection shellResolution: 2.75→2.8 Å / % possible all: 82.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→45.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.868 / SU B: 13.346 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 2480 5.1 %RANDOM
Rwork0.18627 ---
obs0.19039 46347 82.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.01 Å2
2--0.05 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.73→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13146 0 1 263 13410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.95418230
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75451604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46523.869672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.978152386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5191596
X-RAY DIFFRACTIONr_chiral_restr0.1250.21968
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110248
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_it0.6061.58028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.184212948
X-RAY DIFFRACTIONr_scbond_it1.84935438
X-RAY DIFFRACTIONr_scangle_it3.1234.55282
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.731→2.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 121 -
Rwork0.26 2543 -
obs--61.4 %

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