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- PDB-3uva: Crystal structure of L-rhamnose isomerase mutant W38F from Bacill... -

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Basic information

Entry
Database: PDB / ID: 3uva
TitleCrystal structure of L-rhamnose isomerase mutant W38F from Bacillus halodurans in complex with Mn
ComponentsL-Rhamnose isomerase
KeywordsISOMERASE / (beta/alpha)8 barrel
Function / homology
Function and homology information


L-rhamnose isomerase / L-rhamnose isomerase activity / 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: 2.69 Å
AuthorsDoan, T.T.N. / Prabhu, P. / Jeya, M. / Kim, J.K. / 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
DepositionNov 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)196,58612
Polymers196,1474
Non-polymers4408
Water8,161453
1
A: L-Rhamnose isomerase
C: L-Rhamnose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2936
Polymers98,0732
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-43 kcal/mol
Surface area32990 Å2
MethodPISA
2
B: L-Rhamnose isomerase
D: L-Rhamnose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2936
Polymers98,0732
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-45 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.374, 164.779, 92.816
Angle α, β, γ (deg.)90.00, 117.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-Rhamnose isomerase


Mass: 49036.668 Da / Num. of mol.: 4 / Mutation: W38F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: rhaA, BH1552 / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KCL9, L-rhamnose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 57.53 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 6
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: 2.69→50 Å / Num. obs: 53466 / % possible obs: 88.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.692→2.75 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.43 / % possible all: 91.2

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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: 2.69→45.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.87 / SU B: 13.16 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26597 2778 5.1 %RANDOM
Rwork0.18543 ---
all0.18958 53466 --
obs0.18958 51528 87.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.846 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.69→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13188 0 8 453 13649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213519
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.95418296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56251607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07923.867675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.843152403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9621595
X-RAY DIFFRACTIONr_chiral_restr0.1280.21972
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110279
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_it0.6231.58043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.218212977
X-RAY DIFFRACTIONr_scbond_it1.8935476
X-RAY DIFFRACTIONr_scangle_it3.24.55319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.692→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 196 -
Rwork0.25 3510 -
obs--81.99 %

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