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- PDB-3cqk: Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (for... -

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Basic information

Entry
Database: PDB / ID: 3cqk
TitleCrystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (form B) complex with Zn2+ and sulfate
ComponentsL-ribulose-5-phosphate 3-epimerase ulaE
KeywordsISOMERASE / TIM-barrel / phosphate-binding motif / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


L-ribulose-5-phosphate 3-epimerase / L-ribulose-5-phosphate 3-epimerase activity / intramolecular oxidoreductase activity, interconverting aldoses and ketoses / L-ascorbic acid catabolic process
Similarity search - Function
L-ribulose-5-phosphate 3-epimerase / L-ribulose-5-phosphate 3-epimerase, Enterobacteriaceae / 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
L-ribulose-5-phosphate 3-epimerase UlaE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsShi, R. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Bacteriol. / Year: 2008
Title: Structure of L-xylulose-5-Phosphate 3-epimerase (UlaE) from the anaerobic L-ascorbate utilization pathway of Escherichia coli: identification of a novel phosphate binding motif within a TIM barrel fold.
Authors: Shi, R. / Pineda, M. / Ajamian, E. / Cui, Q. / Matte, A. / Cygler, M.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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 / _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_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

Downloads & links

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Assembly

Deposited unit
A: L-ribulose-5-phosphate 3-epimerase ulaE
B: L-ribulose-5-phosphate 3-epimerase ulaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0318
Polymers66,5782
Non-polymers4546
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-157.9 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.028, 132.550, 82.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein L-ribulose-5-phosphate 3-epimerase ulaE / L-xylulose-5- phosphate 3-epimerase / L-ascorbate utilization protein E


Mass: 33288.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: ulaE / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8XDI5, L-ribulose-5-phosphate 3-epimerase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 44.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Li2SO4, pH 8.5, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorDetector: CCD / Date: Aug 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 43820 / % possible obs: 92.4 % / Redundancy: 7 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.001 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.32-2.43.60.34431311.001165.5
2.4-2.54.80.30435841175.8
2.5-2.6160.29141441.004188
2.61-2.756.90.2744960.999194.8
2.75-2.927.50.21947501.0061100
2.92-3.157.80.15647441.0021100
3.15-3.477.90.147431.0011100
3.47-3.977.90.0647110.9991100
3.97-57.90.04476911100
5-507.80.03547481199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CQH

3cqh


Resolution: 2.33→44.24 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.517 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.461 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1151 4.9 %RANDOM
Rwork0.187 ---
obs0.188 23386 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.191 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---1.05 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.33→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 14 82 4480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224484
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9556066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63423.874222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7515774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.981538
X-RAY DIFFRACTIONr_chiral_restr0.0940.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023442
X-RAY DIFFRACTIONr_nbd_refined0.1930.21936
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23022
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2175
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.27
X-RAY DIFFRACTIONr_mcbond_it0.7591.52848
X-RAY DIFFRACTIONr_mcangle_it1.2824392
X-RAY DIFFRACTIONr_scbond_it1.81731912
X-RAY DIFFRACTIONr_scangle_it2.8934.51674
LS refinement shellResolution: 2.326→2.387 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 56 -
Rwork0.21 1186 -
all-1242 -
obs--69.08 %
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)
10.6183-0.1225-0.06080.6193-0.32630.3875-0.0169-0.03090.01880.1702-0.0221-0.038-0.07390.04010.0390.0617-0.0038-0.0232-0.0491-0.0017-0.067225.447958.728722.9149
20.55610.26460.19940.62960.13850.5797-0.04610.0694-0.0572-0.0830.0037-0.05570.14510.10530.04240.05110.04230.0411-0.04130.0047-0.042732.054542.3582-1.292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 28016 - 291
2X-RAY DIFFRACTION2BB5 - 28016 - 291

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