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- PDB-5uqi: E. coli CFT073 c3406 in complex with A5P -

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Basic information

Entry
Database: PDB / ID: 5uqi
TitleE. coli CFT073 c3406 in complex with A5P
ComponentsPhosphosugar isomerase
KeywordsISOMERASE / Sugar isomerase domain / arabinose-5-phosphate / arabinose-5-phosphate isomerase / API
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding / isomerase activity
Similarity search - Function
: / KpsF-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARABINOSE-5-PHOSPHATE / Phosphosugar isomerase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsCech, D.L. / Pratt, A.C. / Woodard, R.W.
CitationJournal: To Be Published
Title: Insights into the mechanism of arabinose-5-phosphate isomerases.
Authors: Cech, D.L. / Pratt, A.C. / Cheng, M. / Barraza, S. / Yep, A. / Holler, T.P. / Woodard, R.W.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: Phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1442
Polymers20,9121
Non-polymers2321
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphosugar isomerase
hetero molecules

A: Phosphosugar isomerase
hetero molecules

A: Phosphosugar isomerase
hetero molecules

A: Phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5778
Polymers83,6494
Non-polymers9294
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area17770 Å2
ΔGint-136 kcal/mol
Surface area24100 Å2
MethodPISA
3
A: Phosphosugar isomerase
hetero molecules

A: Phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2894
Polymers41,8242
Non-polymers4642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5880 Å2
ΔGint-57 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.890, 71.830, 76.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Phosphosugar isomerase


Mass: 20912.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Strain: CFT073 / ATCC 700928 / UPEC / Gene: c3406 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2VCL5
#2: Chemical ChemComp-A5P / ARABINOSE-5-PHOSPHATE


Mass: 232.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dehydrate pH 5.6, 0.5 M NaCl, 2% v/v ethylene imine polymer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.62→17.96 Å / Num. obs: 24950 / % possible obs: 99.3 % / Redundancy: 6.7 % / Net I/σ(I): 6.58

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FXA

3fxa


Resolution: 1.62→17.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.303 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.085
RfactorNum. reflection% reflectionSelection details
Rfree0.20117 1279 5.1 %RANDOM
Rwork0.17992 ---
obs0.18106 23670 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.109 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20 Å2
2--0.02 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.62→17.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 14 106 1525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191442
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.9781954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7242550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32815249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.45153
X-RAY DIFFRACTIONr_chiral_restr0.130.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211026
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8461.985752
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4262.968937
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5062.402689
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.77629.3482167
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.624→1.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 85 -
Rwork0.198 1633 -
obs--94.34 %

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