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Entry
Database: PDB / ID: 6ila
TitleTwo Glycerol complexed Crystal structure of fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi
ComponentsFructuronate-tagaturonate epimerase UxaE
KeywordsISOMERASE / UxaE / TIM-barrel
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesCohnella laeviribosi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsChoi, M.Y. / Kang, L.W. / Ho, T.H. / Nguyen, D.Q. / Lee, I.H. / Lee, J.H. / Park, Y.S. / Park, H.J.
CitationJournal: To be published
Title: Crystal structure of fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi
Authors: Choi, M.Y. / Kang, L.W. / Ho, T.H. / Nguyen, D.Q. / Lee, I.H. / Lee, J.H. / Park, Y.S. / Park, H.J.
History
DepositionOct 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 25, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / atom_type / cell / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _cell.angle_beta / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _struct_asym.entity_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_num_residues / _symmetry.space_group_name_Hall
Description: Ligand identity / Details: The sulfate ion is changed to a phosphate ion. / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Fructuronate-tagaturonate epimerase UxaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5535
Polymers55,2081
Non-polymers3454
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-17 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.269, 51.998, 73.974
Angle α, β, γ (deg.)90.000, 100.656, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Fructuronate-tagaturonate epimerase UxaE


Mass: 55208.102 Da / Num. of mol.: 1 / Mutation: S345A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cohnella laeviribosi (bacteria) / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: EC: 5.1.2.7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsWP_019005805.1 for sequence reference

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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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 8.5
Details: 0.2 M Potassium sodium tartrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.675→50 Å / Num. obs: 14303 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 49.3986650862 Å2 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.075 / Rrim(I) all: 0.192 / Χ2: 4.214 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.69-2.744.50.4966910.720.2480.5571.02196.8
2.74-2.794.70.4737080.7720.2320.5291.02199.2
2.79-2.8450.4647050.7950.2230.5161.0498.9
2.84-2.95.20.4357090.8320.2060.4831.05899.6
2.9-2.965.30.4136990.9060.1920.4571.18199.3
2.96-3.035.60.3677030.9180.1670.4041.40799.7
3.03-3.115.70.3457030.9020.1550.3791.56599.7
3.11-3.195.80.3267050.9290.1450.3571.61399.9
3.19-3.285.90.2697360.9440.1170.2942.122100
3.28-3.396.10.2466890.9590.1050.2682.55599.9
3.39-3.516.10.2397310.9520.1030.2613.07299.9
3.51-3.656.30.2087060.9640.0880.2273.59899.7
3.65-3.826.40.1927170.9790.0810.2084.14100
3.82-4.026.50.1767270.9760.0730.1914.766100
4.02-4.276.70.1677140.9820.0680.1815.598100
4.27-4.66.70.1547090.9820.0630.1666.47399.9
4.6-5.066.70.1537210.9770.0620.1657.217100
5.06-5.796.70.1467310.9830.0590.1586.11799.9
5.79-7.296.60.1327410.9870.0530.1425.462100
7.29-506.90.1097580.9820.0440.11814.85899.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ILB

6ilb


Resolution: 2.69→36.3491624588 Å / SU ML: 0.420136682428 / Cross valid method: THROUGHOUT / σ(F): 1.36875042987 / Phase error: 30.9210339953
RfactorNum. reflection% reflectionSelection details
Rfree0.284320448633 676 4.7276033289 %RANDOM
Rwork0.19913973908 ---
obs0.20316698807 14299 98.4034133921 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.1622809606 Å2
Refinement stepCycle: LAST / Resolution: 2.69→36.3491624588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 18 24 3927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008686412953743979
X-RAY DIFFRACTIONf_angle_d0.9959006269765367
X-RAY DIFFRACTIONf_chiral_restr0.0504375633963576
X-RAY DIFFRACTIONf_plane_restr0.00548051466974704
X-RAY DIFFRACTIONf_dihedral_angle_d7.356304776922373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.88150.3753093584181290.25445890442536X-RAY DIFFRACTION92.6634214186
2.8815-3.17130.3059514819751170.2303725230432731X-RAY DIFFRACTION99.5804195804
3.1713-3.62980.3188443714691360.2008411474162779X-RAY DIFFRACTION99.8971898561
3.6298-4.57180.2592007154751410.1718918490452750X-RAY DIFFRACTION99.9654218534
4.5718-36.3490.2599648334811530.1949342968462827X-RAY DIFFRACTION99.8659517426

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