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- PDB-3p14: Crystal structure of L-rhamnose isomerase with a novel high therm... -

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Basic information

Entry
Database: PDB / ID: 3p14
TitleCrystal structure of L-rhamnose isomerase with a novel high thermo-stability from Bacillus halodurans
ComponentsL-rhamnose isomerase
KeywordsISOMERASE / Tim barrel
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: 2.51 Å
AuthorsDoan, T.T.N. / Prabhu, P. / 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
DepositionSep 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-rhamnose isomerase
B: L-rhamnose isomerase
C: L-rhamnose isomerase
D: L-rhamnose isomerase


Theoretical massNumber of molelcules
Total (without water)196,3034
Polymers196,3034
Non-polymers00
Water8,125451
1
A: L-rhamnose isomerase
C: L-rhamnose isomerase


Theoretical massNumber of molelcules
Total (without water)98,1512
Polymers98,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-18 kcal/mol
Surface area32900 Å2
MethodPISA
2
B: L-rhamnose isomerase
D: L-rhamnose isomerase


Theoretical massNumber of molelcules
Total (without water)98,1512
Polymers98,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-17 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.240, 164.880, 92.010
Angle α, β, γ (deg.)90.00, 115.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-rhamnose isomerase


Mass: 49075.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: ATCC BAA-125 / Gene: BH1552, rhaA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KCL9, L-rhamnose isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% (w/v) PEG 8000, 0.1M HEPES pH 6.0, 0.2M sodium acetate , 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: 1.23999 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23999 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 76165 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.112

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→45.78 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.512 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25551 3751 5 %RANDOM
Rwork0.18506 ---
obs0.18859 70988 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.388 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.51→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13160 0 0 451 13611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02213493
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.95318269
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62951601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43523.858674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.782152393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9931595
X-RAY DIFFRACTIONr_chiral_restr0.1370.21966
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110263
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_it0.8511.58013
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.646212929
X-RAY DIFFRACTIONr_scbond_it2.55135480
X-RAY DIFFRACTIONr_scangle_it4.1754.55340
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.505→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 256 -
Rwork0.263 4988 -
obs--93.16 %

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