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- PDB-2q4t: Ensemble refinement of the protein crystal structure of a cytosol... -

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Basic information

Entry
Database: PDB / ID: 2q4t
TitleEnsemble refinement of the protein crystal structure of a cytosolic 5'-nucleotidase III from Mus musculus Mm.158936
ComponentsCytosolic 5'-nucleotidase III
KeywordsHYDROLASE / Ensemble Refinement / Refinement Methodology Development / UMPH-1 / CYTOSOLIC 5'-NUCLEOTIDASE III / NT5C3 PROTEIN / AAH38029 / BC038029 / MM.158936 / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Pyrimidine catabolism / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase ...Pyrimidine catabolism / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / transferase activity / nuclear body / nucleotide binding / magnesium ion binding / endoplasmic reticulum / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain / Pyrimidine 5'-nucleotidase, eukaryotic / Pyrimidine 5'-nucleotidase (UMPH-1) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain / Pyrimidine 5'-nucleotidase, eukaryotic / Pyrimidine 5'-nucleotidase (UMPH-1) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cytosolic 5'-nucleotidase 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.35 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Structure of Pyrimidine 5'-Nucleotidase Type 1: INSIGHT INTO MECHANISM OF ACTION AND INHIBITION DURING LEAD POISONING.
Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / McCoy, J.G. / Phillips, G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 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 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosolic 5'-nucleotidase III
B: Cytosolic 5'-nucleotidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8044
Polymers68,3282
Non-polymers4772
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.674, 133.674, 38.889
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Number of models4

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Components

#1: Protein Cytosolic 5'-nucleotidase III / cN-III / Pyrimidine 5'-nucleotidase 1 / P5'N-1 / P5N-1 / PN-I / Lupin


Mass: 34163.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Isoform 1 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nt5c3, VSP_021566 / Plasmid: PVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9D020, 5'-nucleotidase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.5 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2BDU.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 2BDU

2bdu


Resolution: 2.35→43.755 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1771130.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2bdu and the first data set in the deposited structure factor file for 2bdu ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2bdu and the first data set in the deposited structure factor file for 2bdu along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 4 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1619 5.1 %RANDOM
Rwork0.173 ---
obs0.173 31910 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.482 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.35→43.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 30 359 5041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.542.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.35-2.50.2782595.20.20847240.0175425498391.9
2.5-2.690.2842745.10.20450720.0175376534699.4
2.69-2.960.3062684.90.1951540.0195436542299.7
2.96-3.390.26326750.18451020.0165377536999.9
3.39-4.270.2372634.90.17651470.01554115410100
4.27-43.760.2072885.40.14650920.0125384538099.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3epe_xplor_par.txt

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