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- PDB-4yih: Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase... -

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Basic information

Entry
Database: PDB / ID: 4yih
TitleCrystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU
Components5'(3')-deoxyribonucleotidase, cytosolic type
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 5'-nucleotidase / dephosphorylation / phosphorylation / HAD-like / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


pyrimidine nucleotide binding / dTMP catabolic process / UMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / dGMP catabolic process / nucleotidase activity / dUMP catabolic process / amide catabolic process / Pyrimidine catabolism ...pyrimidine nucleotide binding / dTMP catabolic process / UMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / dGMP catabolic process / nucleotidase activity / dUMP catabolic process / amide catabolic process / Pyrimidine catabolism / IMP 5'-nucleotidase activity / IMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / dephosphorylation / mitochondrion / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
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-2O2 / PHOSPHATE ION / 5'(3')-deoxyribonucleotidase, cytosolic type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsPachl, P. / Rezacova, P. / Brynda, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic15-05677S Czech Republic
CitationJournal: Medchemcomm / Year: 2015
Title: Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor
Authors: Pachl, P. / Simak, O. / Rezacova, P. / Fabry, M. / Budesinsky, M. / Rosenberg, I. / Brynda, J.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Jan 10, 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_ncs_dom_lim
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_alt_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_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)46,9469
Polymers45,6102
Non-polymers1,3357
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-50 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.818, 46.451, 61.738
Angle α, β, γ (deg.)111.180, 88.160, 104.700
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 4 - 195 / Label seq-ID: 4 - 195

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 22805.162 Da / Num. of mol.: 2 / Fragment: UNP residues 1-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C, DNT1, UMPH2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TCD5, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 5 types, 197 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-2O2 / 1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione


Mass: 502.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N2O11P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 40 mM potassium phosphate monobasic, 6% PEG8000, 20% gycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.82→57.443 Å / Num. obs: 33500 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.11 % / Biso Wilson estimate: 34.274 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.27
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.82-1.930.4622.09117115331194.1
1.93-2.060.2713.611161505395.2
2.06-2.230.1535.9910470472995.8
2.23-2.440.0969.239684438196.3
2.44-2.720.06412.68801398897.1
2.72-3.140.03918.497733350796.9
3.14-3.850.02527.226583298997.3
3.85-5.420.02432.825054229396.7
5.420.0333.422686122992.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREPphasing
PDB_EXTRACT3.11data extraction
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L57

4l57


Resolution: 1.82→57.44 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2253 / WRfactor Rwork: 0.1784 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8166 / SU B: 7.638 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1479 / SU Rfree: 0.1388 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1672 5 %RANDOM
Rwork0.1847 ---
obs0.1868 33458 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.16 Å2 / Biso mean: 36.8837 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.58 Å2-0.2 Å2
2--0.69 Å20.87 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.82→57.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 84 190 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193232
X-RAY DIFFRACTIONr_bond_other_d0.0060.023033
X-RAY DIFFRACTIONr_angle_refined_deg2.0831.9934407
X-RAY DIFFRACTIONr_angle_other_deg1.2563.0056939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.56322.229157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02915520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6751537
X-RAY DIFFRACTIONr_chiral_restr0.1710.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213576
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02781
X-RAY DIFFRACTIONr_mcbond_it1.9872.0631515
X-RAY DIFFRACTIONr_mcbond_other1.9852.0611514
X-RAY DIFFRACTIONr_mcangle_it2.6933.0761889
Refine LS restraints NCS

Ens-ID: 1 / Number: 11304 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 123 -
Rwork0.277 2337 -
all-2460 -
obs--94.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5124-0.2257-0.10180.41680.08650.0805-0.01290.02120.11410.0799-0.01540.01590.01610.03040.02830.1070.02480.00270.0468-0.00150.1647-1.79446.1705-1.1549
21.54820.32710.16340.8067-0.41530.74070.03270.1459-0.18110.05210.03780.04220.03090.0412-0.07050.10440.03150.00550.0421-0.02610.17431.3702-8.622-5.2535
33.0002-0.3284-0.8730.60910.44960.5277-0.0061-0.4378-0.29270.1132-0.01850.017-0.00320.05290.02460.16720.0367-0.00370.09310.07230.17321.3429-9.12639.4198
42.55711.606-1.95212.4087-1.60291.8827-0.07350.7943-0.0951-0.04450.0314-0.14510.1147-0.42560.04220.0143-0.0127-0.00730.417-0.01560.023411.2831-0.5661-34.0712
51.82830.1392-0.65090.5111-0.71781.12780.03630.74060.0691-0.0378-0.117-0.06370.0456-0.04370.08070.01180.0130.01420.41490.01030.058.9826-0.2329-30.6337
60.3924-0.0957-0.22790.4472-0.11150.9182-0.0420.3825-0.06740.06550.0512-0.01220.1511-0.0318-0.00920.04490.0229-0.00240.5049-0.10550.08694.0192-9.3416-24.7311
70.5841-0.3264-1.47190.21320.376710.29050.02870.03610.0451-0.0153-0.016-0.0353-0.1234-0.0562-0.01270.1174-0.00750.0240.0816-0.0060.1398-8.41442.5711-5.2095
81.41140.41645.71670.12781.702223.2057-0.10020.06710.0114-0.0420.04390.0064-0.45490.33970.05620.1064-0.02220.03080.15310.01140.133814.9966-1.3346-24.935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 121
2X-RAY DIFFRACTION2A122 - 162
3X-RAY DIFFRACTION3A163 - 195
4X-RAY DIFFRACTION4B4 - 44
5X-RAY DIFFRACTION5B45 - 94
6X-RAY DIFFRACTION6B95 - 195
7X-RAY DIFFRACTION7A202
8X-RAY DIFFRACTION8B202

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