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- PDB-1hpu: 5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP -

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Basic information

Entry
Database: PDB / ID: 1hpu
Title5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP
Components5'-NUCLEOTIDASE
KeywordsHYDROLASE / metalloenzyme / metallophosphatase / domain rotation / 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 signature 1. / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 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 signature 1. / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / Protein UshA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 13, 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.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 / _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
C: 5'-NUCLEOTIDASE
D: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,25116
Polymers233,1104
Non-polymers2,14012
Water21,9601219
1
A: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8134
Polymers58,2781
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8134
Polymers58,2781
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8134
Polymers58,2781
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8134
Polymers58,2781
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.400, 89.960, 96.260
Angle α, β, γ (deg.)110.79, 106.43, 107.76
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
5'-NUCLEOTIDASE


Mass: 58277.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: USHA / Plasmid: PTRC99A / 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.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-A12 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE


Mass: 425.228 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1219 / 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: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium citrate, lithium chloride, manganese chloride, alpha,beta-methylene-ADP, PEG monomethylether 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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
32 mM1reservoirMnCl2
42 mMAMPCP1reservoir
515 %(w/v)PEG5000 MME1reservoir
615 %(v/v)ethylenediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8445 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1999
RadiationMonochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8445 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 203784 / Num. obs: 203784 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.7
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.39 / % possible all: 93.2
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ush

3ush


Resolution: 1.85→28.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1816055.08 / 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
Rfree0.234 1981 1 %RANDOM
Rwork0.207 ---
obs0.207 198903 97.1 %-
all-198903 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.81 Å2 / ksol: 0.3524 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å2-0.48 Å23.2 Å2
2---3.04 Å24.7 Å2
3---5.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16400 0 116 1219 17735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 295 0.9 %
Rwork0.301 31863 -
obs--94.2 %
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg0.98
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shell
*PLUS
% reflection Rfree: 0.9 %

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