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- PDB-1oid: 5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S2... -

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Basic information

Entry
Database: PDB / ID: 1oid
Title5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S228C, P513C)
ComponentsPROTEIN USHA
KeywordsHYDROLASE / METALLOPROTEIN / DOMAIN MOVEMENT / DISULFIDE ENGINEERING / UDP-SUGAR HYDROLASE / CONFORMATIONAL TRAPPING
Function / homology
Function and homology information


UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / nucleotide catabolic process / 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
NICKEL (II) ION / Protein UshA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / 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 13, 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 1.2Dec 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.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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)118,5743
Polymers118,5152
Non-polymers591
Water13,439746
1
A: PROTEIN USHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3162
Polymers59,2581
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEIN USHA


Theoretical massNumber of molelcules
Total (without water)59,2581
Polymers59,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.496, 93.708, 82.901
Angle α, β, γ (deg.)90.00, 97.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999, -0.018, 0.04), (-0.037, 0.845, -0.533), (-0.024, -0.534, -0.845)
Vector: 3.96666, -0.33696, -1.55155)

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Components

#1: Protein PROTEIN USHA / 5-NUCLEOTIDASE


Mass: 59257.703 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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES CHAINS A, B CYS 228 SER, CYS 513 PRO CATALYTIC ACTIVITY: UDP-SUGAR + H(2)O = ...ENGINEERED RESIDUES CHAINS A, B CYS 228 SER, CYS 513 PRO CATALYTIC ACTIVITY: UDP-SUGAR + H(2)O = UMP + SUGAR 1- PHOSPHATE.
Has protein modificationY
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: 2.7 Å3/Da / Density % sol: 54.3 %
Crystal growpH: 6.5 / Details: 26% PEG 400, 100 MM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54179
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 194970 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 2.78 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.08 / % possible all: 90.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MOLREPphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HP1

1hp1


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.927 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3557 5.1 %RANDOM
Rwork0.166 ---
obs0.169 66489 98.3 %-
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: 36.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20.02 Å2
2---1.47 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 1 746 8920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0218350
X-RAY DIFFRACTIONr_bond_other_d0.0030.027408
X-RAY DIFFRACTIONr_angle_refined_deg2.171.95311298
X-RAY DIFFRACTIONr_angle_other_deg1.105317349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12951046
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_restr0.150.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.029408
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021601
X-RAY DIFFRACTIONr_nbd_refined0.2330.21813
X-RAY DIFFRACTIONr_nbd_other0.2580.28760
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.24807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3550.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3561.55191
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27728333
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.57633159
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5664.52965
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
Rfree0.272 246
Rwork0.187 4409
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)
10.1713-0.0286-0.07310.26670.06490.2772-0.00510.0015-0.00070.00480.0023-0.0017-0.01310.01590.00280.1693-0.0032-0.0020.1469-0.00280.1538164.1651-186.35373.0726
21.36470.17980.14690.64730.01930.1111-0.14090.00210.1764-0.09980.06680.33540.0727-0.0740.07410.0915-0.0272-0.03140.15630.01920.3159130.9891-194.3594.4345
30.2253-0.07540.0080.2078-0.25360.6798-0.0035-0.0141-0.0096-0.0054-0.0204-0.0064-0.03640.02480.02390.154-0.00480.00680.1650.01360.1363176.2435-196.8023
41.53390.41090.1414.7849-1.25010.024-0.05120.0059-0.11290.2708-0.479-1.1513-0.03830.2130.53030.0157-0.0193-0.07320.26570.2680.4719208.9844-203.1952
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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