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- PDB-4wwl: E. coli 5'-nucleotidase mutant I521C labeled with MTSL (intermedi... -

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Basic information

Entry
Database: PDB / ID: 4wwl
TitleE. coli 5'-nucleotidase mutant I521C labeled with MTSL (intermediate form)
ComponentsProtein UshA
KeywordsHYDROLASE / 5NT / Phosphatase / EPR label
Function / homology
Function and homology information


UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / nucleotide catabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / outer membrane-bounded periplasmic space / nucleotide binding / metal ion binding
Similarity search - Function
5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases ...5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Chem-MTN / Protein UshA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsKrug, U. / Paithankar, K.S. / Schultz-Heienbrok, R. / Strater, N.
CitationJournal: To Be Published
Title: E. coli 5'-nucleotidase mutant I521C labeled with MTSL (intermediate form)
Authors: Krug, U. / Paithankar, K.S. / Schultz-Heienbrok, R. / Strater, N.
History
DepositionNov 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 2.0Oct 24, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein UshA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,81116
Polymers59,3391
Non-polymers1,47215
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-163 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.890, 68.890, 307.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-964-

HOH

21A-1072-

HOH

31A-1108-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein UshA / 5'-nucleotidase


Mass: 59338.750 Da / Num. of mol.: 1 / Fragment: UNP residues 26-550
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ushA, b0480, JW0469 / Production host: Escherichia coli (E. coli)
References: UniProt: P07024, UDP-sugar diphosphatase, 5'-nucleotidase

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Non-polymers , 6 types, 442 molecules

#2: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100 mM Bis-Tris pH 5.5, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.23→38.18 Å / Num. obs: 36649 / % possible obs: 97.9 % / Redundancy: 12 % / Biso Wilson estimate: 27.73 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 40.3
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.102 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
AMoREphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HP1

1hp1


Resolution: 2.23→38.18 Å / Cor.coef. Fo:Fc: 0.9435 / Cor.coef. Fo:Fc free: 0.9327 / SU R Cruickshank DPI: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.197 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.148
Details: THR 273 and PRO 274 were set to occupancies of 0.5 due to clashes with their symmetry mates. Electron density for a potential alternative conformation of the respective loop was missing.
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 1147 3.13 %RANDOM
Rwork0.1549 ---
obs0.1559 36647 97.94 %-
Displacement parametersBiso mean: 26.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.0423 Å20 Å20 Å2
2---1.0423 Å20 Å2
3---2.0846 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 2.23→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 73 427 4611
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014268HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085784HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1484SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes128HARMONIC2
X-RAY DIFFRACTIONt_gen_planes609HARMONIC5
X-RAY DIFFRACTIONt_it4268HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion16.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion531SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5348SEMIHARMONIC4
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.1693 88 3.04 %
Rwork0.1515 2810 -
all0.152 2898 -
obs--97.94 %
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)
10.308-0.18120.21920.9081-0.21430.84140.04010.0097-0.0069-0.14590.0156-0.02290.05960.0423-0.0557-0.00830.0025-0.0027-0.076-0.0009-0.030120.77970.907196.7091
20.695-1.9748-0.16081.278-0.64610.76010.0188-0.0403-0.00660.01180.02460.0672-0.1191-0.0027-0.04340.00190.0320.00540.00780.01810.00095.515520.460598.6369
31.5568-0.41040.8140.8992-0.27151.53630.16860.2787-0.0208-0.2832-0.1131-0.10620.05310.2944-0.0555-0.04390.0140.0084-0.06520.007-0.062138.959928.4946101.141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|26 - A|342}
2X-RAY DIFFRACTION2{A|343 - A|362}
3X-RAY DIFFRACTION3{A|363 - A|550}

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