[English] 日本語
Yorodumi
- PDB-4yik: Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yik
TitleCrystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU
Components5'(3')-deoxyribonucleotidase, mitochondrial
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 5'-nucleotidase / dephosphorylation / phosphorylation / HAD-like / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chem-2O2 / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 5'(3')-deoxyribonucleotidase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.483 Å
AuthorsPachl, P. / Rezacova, P. / Brynda, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic 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: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / 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 / _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 / _citation.title
Revision 2.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'(3')-deoxyribonucleotidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,81114
Polymers23,1681
Non-polymers1,64313
Water4,738263
1
A: 5'(3')-deoxyribonucleotidase, mitochondrial
hetero molecules

A: 5'(3')-deoxyribonucleotidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,62228
Polymers46,3372
Non-polymers3,28526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7460 Å2
ΔGint-0 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.870, 73.870, 106.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein 5'(3')-deoxyribonucleotidase, mitochondrial / 5' / 3'-nucleotidase / mitochondrial / Deoxy-5'-nucleotidase 2 / dNT-2


Mass: 23168.391 Da / Num. of mol.: 1 / Fragment: UNP residues 32-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5M, DNT2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NPB1, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

-
Non-polymers , 7 types, 276 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 1 / Source method: obtained synthetically / Formula: C18H20N2O11P2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20 mM potassium phosphate monobasic, 8% PEG8000, 10% gycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.915 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.483→60.641 Å / Num. all: 49438 / Num. obs: 49438 / % possible obs: 100 % / Redundancy: 8 % / Rsym value: 0.065 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueDiffraction-ID% possible all
1.483-1.567.60.74515421971080.7451100
1.56-1.6680.4571.75406467250.457100
1.66-1.778.10.2842.75114363420.284100
1.77-1.918.10.1684.64769659020.168100
1.91-2.18.10.0977.64419154660.097100
2.1-2.348.10.06411.34012149600.064100
2.34-2.718.10.058113569744250.058100
2.71-3.3280.078.13018837760.07100
3.32-4.697.90.03516.72340429800.035100
4.69-28.0497.30.02422.21276517540.02499.5

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.11data extraction
SCALA3.3.16data scaling
REFMAC5.8.0049refinement
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4L6A

4l6a


Resolution: 1.483→60.64 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1775 / WRfactor Rwork: 0.1519 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8952 / SU B: 2.001 / SU ML: 0.037 / SU R Cruickshank DPI: 0.053 / SU Rfree: 0.0554 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1758 2497 5.1 %RANDOM
Rwork0.1528 ---
obs0.154 49321 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.12 Å2 / Biso mean: 22.5767 Å2 / Biso min: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0 Å2
2---0.39 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.483→60.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 92 263 1991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021818
X-RAY DIFFRACTIONr_bond_other_d0.0020.021721
X-RAY DIFFRACTIONr_angle_refined_deg1.9352.0052462
X-RAY DIFFRACTIONr_angle_other_deg0.8853.0013948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.69122.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11715297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7071516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
X-RAY DIFFRACTIONr_mcbond_it1.5391.628824
X-RAY DIFFRACTIONr_mcbond_other1.5381.627825
X-RAY DIFFRACTIONr_mcangle_it2.3772.4321033
LS refinement shellResolution: 1.483→1.522 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 181 -
Rwork0.264 3425 -
all-3606 -
obs--99.94 %
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)
10.5141-0.1767-0.20080.49040.02440.16720.0511-0.02710.0934-0.0632-0.0114-0.0758-0.05860.0313-0.03970.0344-0.01250.02180.0259-0.00710.0293-3.976631.757422.7743
20.42090.1119-0.17490.1621-0.03180.19910.0130.0047-0.0439-0.0116-0.013-0.0443-0.0177-0.002400.01510.00120.01020.0275-0.00280.019-4.555415.587319.3032
30.35510.05550.19250.75170.09771.3732-0.07730.0943-0.0979-0.09110.0819-0.1412-0.02830.1596-0.00460.034-0.01170.04370.0622-0.01940.0597.319911.96511.5474
41.29260.1463-1.92411.77171.27354.13130.03030.0331-0.06590.0703-0.0085-0.14550.0076-0.0575-0.02180.01920.00670.00140.0357-0.00940.0229-3.649624.725628.1179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 106
2X-RAY DIFFRACTION2A107 - 204
3X-RAY DIFFRACTION3A205 - 227
4X-RAY DIFFRACTION4A306

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more