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- PDB-2qlx: Crystal structure of rhamnose mutarotase RhaU of Rhizobium legumi... -

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Basic information

Entry
Database: PDB / ID: 2qlx
TitleCrystal structure of rhamnose mutarotase RhaU of Rhizobium leguminosarum in complex with L-Rhamnose
ComponentsL-rhamnose mutarotase
KeywordsISOMERASE / RhaU / mutarotase / Rhizobium leguminosarum. L-rhamnose / Carbohydrate metabolism / Rhamnose metabolism
Function / homology
Function and homology information


L-rhamnose mutarotase / L-rhamnose mutarotase activity / rhamnose catabolic process / cytoplasm
Similarity search - Function
L-rhamnose mutarotase / Rhamnose/fucose mutarotase / L-rhamnose mutarotase / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / beta-L-rhamnopyranose / L-rhamnose mutarotase
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. trifolii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCarpena, X. / Loewen, P.C.
CitationJournal: J.Bacteriol. / Year: 2008
Title: RhaU of Rhizobium leguminosarum is a rhamnose mutarotase.
Authors: Richardson, J.S. / Carpena, X. / Switala, J. / Perez-Luque, R. / Donald, L.J. / Loewen, P.C. / Oresnik, I.J.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Jul 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_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_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.pdbx_leaving_atom_flag / _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 1.4Aug 30, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-rhamnose mutarotase
B: L-rhamnose mutarotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,78221
Polymers25,7152
Non-polymers1,06719
Water3,675204
1
A: L-rhamnose mutarotase
B: L-rhamnose mutarotase
hetero molecules

A: L-rhamnose mutarotase
B: L-rhamnose mutarotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,56442
Polymers51,4294
Non-polymers2,13538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area13580 Å2
ΔGint-93 kcal/mol
Surface area18950 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-35 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.652, 68.652, 100.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-373-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 1 - 103 / Label seq-ID: 3 - 105

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein L-rhamnose mutarotase / Rhamnose 1-epimerase / Type-3 mutarotase


Mass: 12857.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: rhaM, rhaU / Production host: Escherichia coli (E. coli)
References: UniProt: Q7BSH1, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: 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.: 2 / 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M Sodium Formate, 0.1M Sodium Acetate pH 4.6, 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 23317 / Num. obs: 23317 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.093 / Χ2: 1.051
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2169 / Χ2: 1 / % possible all: 92.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
DNAdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QLW

2qlw


Resolution: 2→28.51 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.428 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 942 5.1 %RANDOM
Rwork0.135 ---
all0.138 18417 --
obs0.138 18417 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 69 204 2021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211969
X-RAY DIFFRACTIONr_bond_other_d0.0030.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9662657
X-RAY DIFFRACTIONr_angle_other_deg1.8633293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4525230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06424.30193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3615361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.664159
X-RAY DIFFRACTIONr_chiral_restr0.1440.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022070
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_nbd_refined0.2380.2381
X-RAY DIFFRACTIONr_nbd_other0.210.21400
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2918
X-RAY DIFFRACTIONr_nbtor_other0.0960.2951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.223
X-RAY DIFFRACTIONr_mcbond_it1.5111.51383
X-RAY DIFFRACTIONr_mcbond_other0.3411.5445
X-RAY DIFFRACTIONr_mcangle_it1.8221853
X-RAY DIFFRACTIONr_scbond_it3.0933914
X-RAY DIFFRACTIONr_scangle_it4.3934.5796
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1386 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.465
LOOSE THERMAL1.5410
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 64 -
Rwork0.133 1281 -
obs-1345 99.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.801-0.0913-0.41791.10420.55721.194-0.01690.0175-0.08320.0979-0.1240.15890.0974-0.13750.1408-0.0404-0.01190.0123-0.0319-0.0255-0.00483.410116.640410.8476
20.8041-0.3672-0.12611.439-0.48670.9413-0.00560.10590.0691-0.025-0.0653-0.1101-0.01770.01460.071-0.04280.0024-0.013-0.04690.001-0.037614.503226.8217-5.2403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 106
2X-RAY DIFFRACTION2B0 - 106

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