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- PDB-4gji: Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mu... -

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Basic information

Entry
Database: PDB / ID: 4gji
TitleCrystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with L-rhamnopyranose
ComponentsL-rhamnose isomerase
KeywordsISOMERASE / Tim Barrel / Sugar binding / Metal binding
Function / homology
Function and homology information


L-rhamnose isomerase activity / L-lyxose metabolic process / rhamnose catabolic process / 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-L-rhamnopyranose / beta-L-rhamnopyranose / L-RHAMNOSE / L-rhamnose isomerase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYoshida, H. / Kamitori, S.
Citation
Journal: FEBS Open Bio / Year: 2013
Title: Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site.
Authors: Yoshida, H. / Yoshihara, A. / Teraoka, M. / Yamashita, S. / 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.
#2: 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.
#3: Journal: Protein Eng.Des.Sel. / Year: 2010
Title: Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of Pseudomonas stutzeri L-rhamnose isomerase.
Authors: Yoshida, H. / Takeda, K. / Izumori, K. / Kamitori, S.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,27725
Polymers191,9224
Non-polymers2,35521
Water35,3811964
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29050 Å2
ΔGint-129 kcal/mol
Surface area51780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.124, 104.917, 112.376
Angle α, β, γ (deg.)90.00, 106.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-rhamnose isomerase


Mass: 47980.570 Da / Num. of mol.: 4 / Fragment: TIM barrel / Mutation: D150N, H101N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: L-RhI / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q75WH8, L-rhamnose isomerase

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Sugars , 3 types, 11 molecules

#2: Sugar
ChemComp-RNS / L-RHAMNOSE


Type: L-saccharide / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
#3: Sugar
ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-RM4 / beta-L-rhamnopyranose / beta-L-rhamnose / 6-deoxy-beta-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LRhapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-rhamnopyranoseCOMMON NAMEGMML 1.0
b-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 1974 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1964 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsRM4 501 AND RNS 502 ARE IN ALTERNATE CONFORMATIONS IN CHAINS B AND D.

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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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 7-8% (w/v) PEG 20000, 50mM MES pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 17, 2011 / Details: mirrors
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 182769 / Num. obs: 182769 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.9 / Num. unique all: 9074 / % possible all: 97.8

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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
Resolution: 1.7→31.48 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 157137.35 / 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
Rfree0.195 17191 9.9 %RANDOM
Rwork0.175 ---
all0.177 173095 --
obs0.175 173095 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.0989 Å2 / ksol: 0.391326 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å20 Å2-1.3 Å2
2---1.15 Å20 Å2
3---3.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13056 0 131 1964 15151
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 2620 9.7 %
Rwork0.221 24342 -
obs-24342 88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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