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- PDB-1ho5: 5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE AND PHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1ho5
Title5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE AND PHOSPHATE
Components5'-NUCLEOTIDASE
KeywordsHYDROLASE / metalloprotein / domain movement
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
ADENOSINE / : / PHOSPHATE ION / Protein UshA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKnoefel, T. / Straeter, N.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
Authors: Knofel, T. / Strater, 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
DepositionDec 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)117,49910
Polymers116,5552
Non-polymers9448
Water6,395355
1
A: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7505
Polymers58,2781
Non-polymers4724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7505
Polymers58,2781
Non-polymers4724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.900, 75.700, 221.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 5'-NUCLEOTIDASE


Mass: 58277.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: USHA / Production host: Escherichia coli (E. coli) / Strain (production host): DS956
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium citrate, lithium chloride, potassium phosphate, adenosine, manganese chloride, PEG monomethylether 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Knofel, T., (2001) J.Mol.Biol., 309, 255.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMsodium citrate1reservoirpH6.0
280 mM1reservoirLiCl
35 mM1reservoirKH2PO4
45 mMadenosine1reservoir
510 mM1reservoirMnCl2
616 %(w/v)PEG5000 MME1reservoir
725 %(v/v)ethylenediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 25, 1999
RadiationMonochromator: bent single-crystal germanium triangular monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 69235 / Num. obs: 69235 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.298 / % possible all: 97.2
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ush

1ush


Resolution: 2.1→29.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2757655.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2116 3.1 %RANDOM
Rwork0.238 ---
all0.238 69235 --
obs0.238 69235 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2 Å2 / ksol: 0.3247 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å20 Å20 Å2
2---4.85 Å20 Å2
3---0.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8200 0 52 355 8607
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 367 3.2 %
Rwork0.269 11035 -
obs-11035 99.9 %
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.324 / Rfactor Rwork: 0.269

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