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- PDB-1mh9: Crystal Structure Analysis of deoxyribonucleotidase -

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Basic information

Entry
Database: PDB / ID: 1mh9
TitleCrystal Structure Analysis of deoxyribonucleotidase
Componentsdeoxyribonucleotidase
KeywordsHYDROLASE / Rossmann fold / 4-helix bundle
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide catabolic process / nucleotidase activity / dUMP catabolic process / Pyrimidine catabolism / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / DNA replication / mitochondrial matrix / nucleotide binding / mitochondrion / metal ion binding
Similarity search - Function
5'(3')-deoxyribonucleotidase / 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) / Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...5'(3')-deoxyribonucleotidase / 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) / Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 5'(3')-deoxyribonucleotidase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsRinaldo-Matthis, A. / Rampazzo, C. / Reichard, P. / Bianchi, V. / Nordlund, P.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Crystal structure of a human mitochondrial deoxyribonucleotidase.
Authors: Rinaldo-Matthis, A. / Rampazzo, C. / Reichard, P. / Bianchi, V. / Nordlund, P.
History
DepositionAug 19, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: deoxyribonucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9603
Polymers22,8411
Non-polymers1192
Water6,467359
1
A: deoxyribonucleotidase
hetero molecules

A: deoxyribonucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9216
Polymers45,6822
Non-polymers2394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)73.965, 73.965, 105.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe second part of the biological assembly is generated by the two fold axis: (-Y,-X,-Z+1/2) dx= 1 dy= 1 dz= 0 distance= 2.746

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Components

#1: Protein deoxyribonucleotidase / mitochondrial 5'(3')-deoxyribonucleotidase


Mass: 22841.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPB1, 5'-nucleotidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG 8000, potassium phosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.5
220 %(v/v)glycerol1drop
32 mMdithiothreitol1drop
41 mMEDTA1drop
575 mM1dropNaCl
613 mg/mlprotein1drop
715-25 %(w/v)PEG80001reservoir
80.05 M1reservoirpH5.3K2H2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.03 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2001
RadiationMonochromator: Si (111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 27389 / Num. obs: 27898 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 15.6 Å2
Reflection shellResolution: 1.65→1.71 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 20 Å / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.346

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.64 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2046240.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1375 5 %RANDOM
Rwork0.159 ---
obs0.159 27389 98.7 %-
all-264817 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.8295 Å2 / ksol: 0.387786 e/Å3
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 6 359 1963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.025
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.45
X-RAY DIFFRACTIONc_mcbond_it4.051.5
X-RAY DIFFRACTIONc_mcangle_it4.822
X-RAY DIFFRACTIONc_scbond_it6.842
X-RAY DIFFRACTIONc_scangle_it9.092.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.235 189 4.7 %
Rwork0.178 3838 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 19.64 Å / Num. reflection obs: 26015 / Rfactor obs: 0.159 / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.45
LS refinement shell
*PLUS
Rfactor Rfree: 0.235 / Rfactor Rwork: 0.178

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