[English] 日本語
Yorodumi
- PDB-6g22: Crystal structure of human mitochondrial 5'(3')-deoxyribonucleoti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g22
TitleCrystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PEU
Components5'(3')-deoxyribonucleotidase, mitochondrial
KeywordsHYDROLASE / 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 / BETA-MERCAPTOETHANOL / 5'(3')-deoxyribonucleotidase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.85 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 22, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id

-
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)24,0606
Polymers23,2721
Non-polymers7895
Water4,252236
1
A: 5'(3')-deoxyribonucleotidase, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)48,12112
Polymers46,5432
Non-polymers1,57810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3580 Å2
ΔGint-14 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.753, 73.753, 106.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-585-

HOH

21A-629-

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: 23271.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5M, DNT2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NPB1, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

-
Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 20 mM potassium phosphate monobasic, 8% PEG8000, 10% gycerol, pH 4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.85→43.19 Å / Num. obs: 47028 / % possible obs: 97.9 % / Redundancy: 3.35 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.058 / Net I/σ(I): 15.03
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 1.77 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 7578 / CC1/2: 0.708 / Rrim(I) all: 0.588 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4YIK

4yik


Resolution: 1.85→43.19 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.467 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19069 1264 5 %RANDOM
Rwork0.15534 ---
obs0.15706 24012 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.85→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 50 236 1870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021713
X-RAY DIFFRACTIONr_bond_other_d0.0070.021567
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9852334
X-RAY DIFFRACTIONr_angle_other_deg0.9823.0063640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62423.25383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91815280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4211513
X-RAY DIFFRACTIONr_chiral_restr0.1610.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3492.471781
X-RAY DIFFRACTIONr_mcbond_other2.342.466780
X-RAY DIFFRACTIONr_mcangle_it3.2973.684977
X-RAY DIFFRACTIONr_mcangle_other3.2973.689978
X-RAY DIFFRACTIONr_scbond_it3.1312.81932
X-RAY DIFFRACTIONr_scbond_other3.132.81933
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7244.0791353
X-RAY DIFFRACTIONr_long_range_B_refined6.33830.2982076
X-RAY DIFFRACTIONr_long_range_B_other6.14229.5092013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 91 -
Rwork0.274 1743 -
obs--97.66 %

+
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://pdbjlvh1.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