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- PDB-3ito: Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mu... -

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Basic information

Entry
Database: PDB / ID: 3ito
TitleCrystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant D327N in complex with D-psicose
ComponentsL-rhamnose isomerase
KeywordsISOMERASE / METAL-BINDING PROTEIN / BETA/ALPHA BARREL / HOMO-TETRAMER / TIM barrel
Function / homology
Function and homology information


isomerase activity / metal ion binding
Similarity search - Function
L-rhamnose catabolism isomerase / : / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / alpha-D-psicofuranose / L-rhamnose isomerase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYoshida, H. / Yamaji, M. / Ishii, T. / Izumori, K. / Kamitori, S.
Citation
Journal: Febs J. / Year: 2010
Title: Catalytic reaction mechanism of Pseudomonas stutzeri l-rhamnose isomerase deduced from X-ray structures
Authors: Yoshida, H. / Yamaji, M. / Ishii, T. / Izumori, K. / Kamitori, S.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity
Authors: Yoshida, H. / Yamada, M. / Ohyama, Y. / Takada, G. / Izumori, K. / Kamitori, S.
History
DepositionAug 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.type / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)193,17516
Polymers192,0154
Non-polymers1,16012
Water25,8701436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24030 Å2
ΔGint-123 kcal/mol
Surface area52210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.762, 104.732, 115.035
Angle α, β, γ (deg.)90.00, 108.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-rhamnose isomerase


Mass: 48003.629 Da / Num. of mol.: 4 / Mutation: D150N, D327N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q75WH8, 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: Sugar
ChemComp-PSV / alpha-D-psicofuranose / alpha-D-psicose / D-psicose / psicose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DPsifaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-psicofuranoseCOMMON NAMEGMML 1.0
a-D-PsifIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
PsiSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1436 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 7-8% (W/V) polyethylene glycol 20000, 50mM MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 128987 / Num. obs: 128987 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.4 / % possible all: 96.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HCV

2hcv


Resolution: 1.9→42.15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 28752.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 12186 10 %RANDOM
Rwork0.176 ---
all0.179 122222 --
obs0.176 122222 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.5804 Å2 / ksol: 0.379471 e/Å3
Displacement parametersBiso mean: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-1.85 Å2
2---0.09 Å20 Å2
3---1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13072 0 56 1436 14564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.75
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 1930 10.1 %
Rwork0.228 17153 -
obs-1930 86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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