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- PDB-6g2n: Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase... -

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Basic information

Entry
Database: PDB / ID: 6g2n
TitleCrystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PAU
Components5'(3')-deoxyribonucleotidase, cytosolic type
KeywordsHYDROLASE / 5'-nucleotidase / dephosphorylation / phosphorylation / HAD-like / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


pyrimidine nucleotide binding / dTMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / nucleotidase activity / UMP catabolic process / dUMP catabolic process / amide catabolic process / Pyrimidine catabolism / dGMP catabolic process ...pyrimidine nucleotide binding / dTMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / nucleotidase activity / UMP catabolic process / dUMP catabolic process / amide catabolic process / Pyrimidine catabolism / dGMP catabolic process / : / IMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / dephosphorylation / mitochondrion / extracellular exosome / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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
Chem-O84 / 5'(3')-deoxyribonucleotidase, cytosolic type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsPachl, P. / Rezacova, P. / Brynda, J.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic203-09-0820 Czech Republic
Grant Agency of the Czech Republic15-05677S Czech Republic
Czech Science Foundation17-12703S Czech Republic
CitationJournal: Eur.J.Org.Chem. / Year: 2018
Title: Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases
Authors: Pachl, P. / Simak, O. / Budesinsky, M. / Brynda, J. / Rosenberg, I. / Rezacova, P.
History
DepositionMar 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'(3')-deoxyribonucleotidase, cytosolic type
B: 5'(3')-deoxyribonucleotidase, cytosolic type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8226
Polymers47,7412
Non-polymers1,0814
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-11 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.877, 47.231, 61.795
Angle α, β, γ (deg.)67.860, 88.690, 77.370
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 5'(3')-deoxyribonucleotidase, cytosolic type / Cytosolic 5' / 3'-pyrimidine nucleotidase / Deoxy-5'-nucleotidase 1 / dNT-1


Mass: 23870.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CME is beta-mercapto ethanol covalently bound to cystein residue
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C, DNT1, UMPH2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8TCD5, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-O84 / [(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-[(~{E})-3-phosphonoprop-1-enyl]pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid


Mass: 516.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: Morpheus H2, 0.1M MES/imidazole pH 6.5, 10% PEG 8000, 20% ethylene glycol, 0.02M of each amino acid,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→42.41 Å / Num. obs: 68116 / % possible obs: 87.8 % / Redundancy: 2.22 % / Biso Wilson estimate: 27.42 Å2 / CC1/2: 1 / Rrim(I) all: 0.026 / Net I/σ(I): 18.84
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 2.21 % / Num. unique obs: 11048 / CC1/2: 0.7414 / Rrim(I) all: 0.556 / % possible all: 87.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.546
Highest resolutionLowest resolution
Rotation42.87 Å1.87 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YIH

4yih


Resolution: 1.4→42.41 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.966 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0712 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.066
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2100 3.1 %RANDOM
Rwork0.1508 ---
obs0.1521 66015 87.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.88 Å2 / Biso mean: 27.295 Å2 / Biso min: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-1.14 Å20.09 Å2
2--1.7 Å20.22 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 1.4→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 70 294 3493
Biso mean--23.48 34.23 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193300
X-RAY DIFFRACTIONr_bond_other_d0.0010.023041
X-RAY DIFFRACTIONr_angle_refined_deg2.022.0014510
X-RAY DIFFRACTIONr_angle_other_deg1.96637010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.57422.346162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10915532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9611538
X-RAY DIFFRACTIONr_chiral_restr0.1850.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213612
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02726
X-RAY DIFFRACTIONr_rigid_bond_restr6.10536341
X-RAY DIFFRACTIONr_sphericity_free16.0345194
X-RAY DIFFRACTIONr_sphericity_bonded8.00356355
LS refinement shellResolution: 1.404→1.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 155 -
Rwork0.346 4886 -
all-5041 -
obs--87.23 %

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