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- PDB-1oi8: 5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (P9... -

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Basic information

Entry
Database: PDB / ID: 1oi8
Title5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (P90C, L424C)
ComponentsPROTEIN USHA
KeywordsHYDROLASE / METALLOPROTEIN / DOMAIN MOVEMENT / DISULFIDE ENGINEERING / UDP-SUGAR HYDROLASE
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 / : / Protein UshA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchultz-Heienbrok, R. / Maier, T. / Straeter, N.
Citation
Journal: Protein Sci. / Year: 2004
Title: Trapping a 96 Degree Domain Rotation in Two Distinct Conformations by Engineered Disulfide Bridges
Authors: Schultz-Heienbrok, R. / Maier, T. / Straeter, N.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: E. Coli 5'-Nucleotidase Undergoes a Hinge-Bending Domain Rotation Resembling a Ball-and-Socket Motion
Authors: Knoefel, T. / Straeter, N.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: X-Ray Structure of the Escherichia Coli Periplasmic 5'-Nucleotidase Containing a Dimetal Catalytic Site
Authors: Knoefel, T. / Straeter, N.
History
DepositionJun 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN USHA
B: PROTEIN USHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,99510
Polymers118,4632
Non-polymers5328
Water16,502916
1
A: PROTEIN USHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4985
Polymers59,2321
Non-polymers2664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEIN USHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4985
Polymers59,2321
Non-polymers2664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.689, 97.689, 312.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99757, 0.06973, 0.00119), (-0.06973, 0.9971, 0.0305), (0.00094, -0.03051, 0.99953)
Vector: -51.37434, 51.03961, 0.65184)

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Components

#1: Protein PROTEIN USHA / 5-NUCLEOTIDASE


Mass: 59231.625 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: DISULFIDE CROSSLINK BETWEEN N- AND C-TERMINAL DOMAINS
Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566
References: UniProt: P07024, 5'-nucleotidase, UDP-sugar diphosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES CHAINS A, B PRO 90 CYS, LEU 424 CYS
Sequence detailsADDITIONAL GLU AND 6X HIS AT C-TERMINUS

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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: 3.2 Å3/Da / Density % sol: 61.4 %
Crystal growpH: 8
Details: 1.8 M LI2SO4, 100MM TRIS, 1MM MNCL, 10 MM BETAINE, 10% 2-METHYL-2,4-PENTANDIOLE, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8453
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 2002 / Details: MIRRORS, TRIANGULAR MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 89316 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 4.7 / % possible all: 95.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
BEASTphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HO5

1ho5


Resolution: 2.1→19.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.674 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY AROUND WATER MOLECULES 921 AND 922 COULD ALSO BE EXPLAINED BY OTHER REAGENTS PRESENT IN THE CRYSTALLISATION BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4255 5 %RANDOM
Rwork0.156 ---
obs0.159 80645 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8194 0 22 916 9132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0218386
X-RAY DIFFRACTIONr_bond_other_d0.0020.027410
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.95311346
X-RAY DIFFRACTIONr_angle_other_deg0.922317356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58151048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029448
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021608
X-RAY DIFFRACTIONr_nbd_refined0.2080.21736
X-RAY DIFFRACTIONr_nbd_other0.2520.28845
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.24922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2744
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.971.55208
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75428350
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.93333178
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7094.52996
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 312
Rwork0.191 5849
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)
10.2277-0.19340.00780.34050.10050.12070.04110.05530.0113-0.0047-0.0335-0.02310.01370.0029-0.00760.04240.0384-0.00530.0694-0.00240.040863.328816.993920.2982
20.1204-0.09180.00420.37560.14640.14620.02350.06460.0168-0.0556-0.0646-0.0069-0.05660.01980.0410.04340.0057-0.0110.0640.02830.066755.726947.944625.2279
30.2526-0.12550.17220.196-0.02070.45050.0110.01290.0091-0.0177-0.0143-0.00840.07420.05420.00320.06570.05750.00980.05020.0080.038113.308263.51420.3524
4-0.0666-0.04910.03770.28950.13010.4461-0.00450.0311-0.0152-0.0513-0.02450.0021-0.11630.07910.0290.0542-0.0202-0.00770.06860.01820.05617.387996.17324.4382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 340
2X-RAY DIFFRACTION2A360 - 550
3X-RAY DIFFRACTION3B26 - 340
4X-RAY DIFFRACTION4B360 - 550

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