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- PDB-2ush: 5'-NUCLEOTIDASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 2ush
Title5'-NUCLEOTIDASE FROM E. COLI
Components5'-NUCLEOTIDASE
KeywordsHYDROLASE / 5'-NUCLEOTIDASE / UDP-SUGAR HYDROLASE / PHOSPHATASE / HYDROLASE (PHOSPHORIC MONOESTER) / PERIPLASMIC PROTEIN
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
TUNGSTATE(VI)ION / Protein UshA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.22 Å
AuthorsKnofel, T. / Strater, N.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site.
Authors: Knofel, T. / Strater, N.
#1: Journal: Nucleic Acids Res. / Year: 1986
Title: Nucleotide Sequence and Transcriptional Analysis of the E. Coli Usha Gene, Encoding Periplasmic Udp-Sugar Hydrolase (5'-Nucleotidase): Regulation of the Usha Gene, and the Signal Sequence of ...Title: Nucleotide Sequence and Transcriptional Analysis of the E. Coli Usha Gene, Encoding Periplasmic Udp-Sugar Hydrolase (5'-Nucleotidase): Regulation of the Usha Gene, and the Signal Sequence of its Encoded Protein Product
Authors: Burns, D.M. / Beacham, I.R.
History
DepositionSep 24, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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: 5'-NUCLEOTIDASE
B: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,37015
Polymers121,7902
Non-polymers1,58013
Water2,468137
1
A: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7178
Polymers60,8951
Non-polymers8237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6527
Polymers60,8951
Non-polymers7576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.210, 116.290, 132.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.978658, -0.030984, -0.203148), (0.042549, -0.997698, -0.052808), (-0.201044, -0.060325, 0.977723)
Vector: 104.7029, 113.68778, 12.77432)

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Components

#1: Protein 5'-NUCLEOTIDASE / UDP-SUGAR HYDROLASE


Mass: 60894.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: USHA / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P07024, 5'-nucleotidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: WO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
25 mMTris-HCl1drop
320 mM1dropKCl
40.05 mM1dropZnCl2
5100 mMMES1reservoir
615 mM1reservoirZnSO4
74 mM1reservoirNa2WO4
820 %(v/v)mPEG5501reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→30 Å / Num. obs: 70373 / % possible obs: 98.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 27.8 Å2 / Rsym value: 0.073 / Net I/σ(I): 13
Reflection shellResolution: 2.22→2.27 Å / Redundancy: 4.2 % / Rsym value: 0.35 / % possible all: 95.1
Reflection
*PLUS
Num. measured all: 196559 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 95.1 % / Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
MLPHAREphasing
SHARPphasing
X-PLOR3.851refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.22→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3507 5.1 %RANDOM
Rwork0.198 ---
obs0.198 68946 98.2 %-
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.222 Å20 Å20 Å2
2---4.294 Å20 Å2
3---7.167 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.22→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8014 0 29 137 8180
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.05
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it3
X-RAY DIFFRACTIONx_scangle_it3.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.22→2.36 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 572 5.2 %
Rwork0.291 10340 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.05

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