[English] 日本語
Yorodumi
- PDB-4p5e: CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p5e
TitleCRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE
Components2'-deoxynucleoside 5'-phosphate N-hydrolase 1
KeywordsHYDROLASE / RCL / DNPH1 / Inhibitor / Rossmann Fold
Function / homology
Function and homology information


purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / Purine catabolism / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome ...purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / Purine catabolism / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N6P / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPadilla, A. / Labesse, G. / Kaminski, P.A.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05-01 France
Citation
Journal: Eur.J.Med.Chem. / Year: 2014
Title: 6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: Synthesis, structural studies and cytotoxic activities.
Authors: Amiable, C. / Paoletti, J. / Haouz, A. / Padilla, A. / Labesse, G. / Kaminski, P.A. / Pochet, S.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: Structure of the oncoprotein Rcl bound to three nucleotide analogues.
Authors: Padilla, A. / Amiable, C. / Pochet, S. / Kaminski, P.A. / Labesse, G.
History
DepositionMar 16, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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_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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
B: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3735
Polymers34,4172
Non-polymers9573
Water6,972387
1
B: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules

A: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3735
Polymers34,4172
Non-polymers9573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2990 Å2
ΔGint-39 kcal/mol
Surface area11800 Å2
MethodPISA
2
A: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules

B: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3735
Polymers34,4172
Non-polymers9573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2990 Å2
ΔGint-39 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.974, 52.284, 54.454
Angle α, β, γ (deg.)90.00, 104.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 / c-Myc-responsive protein RCL


Mass: 17208.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Bli5
References: UniProt: O43598, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-N6P / 6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine / 6-Naphthylpurine riboside 5'-monophosphate


Mass: 458.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N4O7P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3K, 200 MM CALCIUM ACETATE, 100 MM TRIS, PH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8103 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8103 Å / Relative weight: 1
ReflectionResolution: 1.35→47.36 Å / Num. obs: 58489 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.5
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FYI

4fyi


Resolution: 1.35→47.357 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 2957 5.06 %
Rwork0.155 --
obs0.1563 58476 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→47.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 65 387 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092473
X-RAY DIFFRACTIONf_angle_d1.3113357
X-RAY DIFFRACTIONf_dihedral_angle_d17.339937
X-RAY DIFFRACTIONf_chiral_restr0.064365
X-RAY DIFFRACTIONf_plane_restr0.007435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37210.25991450.21822644X-RAY DIFFRACTION100
1.3721-1.39580.23271530.22722589X-RAY DIFFRACTION100
1.3958-1.42120.25021180.20232637X-RAY DIFFRACTION100
1.4212-1.44850.23961330.20122632X-RAY DIFFRACTION100
1.4485-1.47810.21641410.18412654X-RAY DIFFRACTION100
1.4781-1.51020.20321490.18012615X-RAY DIFFRACTION100
1.5102-1.54540.21421670.17412608X-RAY DIFFRACTION100
1.5454-1.5840.19631410.1642644X-RAY DIFFRACTION100
1.584-1.62690.18751480.16092616X-RAY DIFFRACTION100
1.6269-1.67470.19781400.16222651X-RAY DIFFRACTION100
1.6747-1.72880.21181090.16332625X-RAY DIFFRACTION100
1.7288-1.79060.20031440.15742655X-RAY DIFFRACTION100
1.7906-1.86230.16281240.14932662X-RAY DIFFRACTION100
1.8623-1.9470.17911600.15422636X-RAY DIFFRACTION100
1.947-2.04970.19861380.14842627X-RAY DIFFRACTION100
2.0497-2.17810.20381220.14512674X-RAY DIFFRACTION100
2.1781-2.34630.1681410.14332646X-RAY DIFFRACTION100
2.3463-2.58240.16361680.14642629X-RAY DIFFRACTION100
2.5824-2.9560.17041260.14792658X-RAY DIFFRACTION100
2.956-3.7240.15141420.1362697X-RAY DIFFRACTION100
3.724-47.3860.15411480.14672720X-RAY DIFFRACTION100
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)
11.9301-0.1657-0.04161.0640.2391.097-0.03130.1595-0.1174-0.06690.01180.07080.0607-0.06250.0220.0675-0.0038-0.0040.0709-0.00390.05344.3321-1.15748.1076
21.6333-0.00680.211.02740.27091.199-0.0267-0.09650.11040.04420.0413-0.0643-0.08120.0743-0.01680.06290.0014-0.00640.0798-0.01090.0552-25.779810.390518.0236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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