[English] 日本語
Yorodumi
- PDB-8qhr: Crystal structure of the human DNPH1 glycosyl-enzyme intermediate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qhr
TitleCrystal structure of the human DNPH1 glycosyl-enzyme intermediate
Components2'-deoxynucleoside 5'-phosphate N-hydrolase 1
KeywordsHYDROLASE / DNPH1 / N-glycosidase / hmdUMP / dRP
Function / homology
Function and homology information


deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / purine nucleotide catabolic process / nucleoside salvage / Purine catabolism / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome ...deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / purine nucleotide catabolic process / 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 / cytoplasm / cytosol
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase
Similarity search - Domain/homology
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRzechorzek, N.J. / West, S.C.
Funding support United Kingdom, European Union, Switzerland, 6items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
Cancer Research UKCC2098 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2098 United Kingdom
Wellcome TrustCC2098 United Kingdom
European Research Council (ERC)ERC-ADG-666400European Union
Louis-Jeantet Foundation Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1.
Authors: Rzechorzek, N.J. / Kunzelmann, S. / Purkiss, A.G. / Silva Dos Santos, M. / MacRae, J.I. / Taylor, I.A. / Fugger, K. / West, S.C.
History
DepositionSep 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

-
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)33,4777
Polymers32,6752
Non-polymers8035
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.420, 55.039, 103.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and resid 41)
d_2ens_1(chain "A" and resid 41)
d_1ens_2(chain "B" and resid 80)
d_2ens_2(chain "A" and resid 80)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ARGARGARGARGBB4126
d_2ens_1ARGARGARGARGAA4126
d_1ens_2ASPASPASPASPBB8065
d_2ens_2ASPASPASPASPAA8065

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.172239160929, -0.016095478512, -0.984923655424), (0.0269712773718, -0.999568690962, 0.0116181859781), (-0.984685849212, -0.0245635424961, 0.172598988238)1.65048812894, -34.8632496835, 1.17389432503
2given(-0.223752314795, 0.0213397820708, -0.974412394895), (-0.0525074968816, -0.998572327535, -0.0098116997796), (-0.973230632684, 0.0489685652485, 0.224553368317)4.60395603894, -34.0660606244, 4.1536774296

-
Components

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


Mass: 16337.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Production host: Escherichia coli (E. coli)
References: UniProt: O43598, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-3DR / 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE / ABASIC DIDEOXYRIBOSE


Type: DNA linking / Mass: 198.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris propane pH 6.5, 16% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.65→103.98 Å / Num. obs: 33501 / % possible obs: 99.8 % / Redundancy: 8.4 % / Biso Wilson estimate: 19.12 Å2 / CC1/2: 0.994 / Net I/σ(I): 5.6
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1625 / CC1/2: 0.164 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
pointless1.12.8data scaling
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→51.97 Å / SU ML: 0.2213 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.3285
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2218 1675 5.02 %
Rwork0.1845 31716 -
obs0.1864 33391 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.95 Å2
Refinement stepCycle: LAST / Resolution: 1.65→51.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 51 287 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272323
X-RAY DIFFRACTIONf_angle_d0.64143149
X-RAY DIFFRACTIONf_chiral_restr0.0421328
X-RAY DIFFRACTIONf_plane_restr0.0099410
X-RAY DIFFRACTIONf_dihedral_angle_d6.3814384
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBX-RAY DIFFRACTIONTorsion NCS0.140346381522
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.0937142245289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.33661370.3432575X-RAY DIFFRACTION98.4
1.7-1.750.39751260.31612586X-RAY DIFFRACTION99.09
1.75-1.820.29791330.29652620X-RAY DIFFRACTION99.42
1.82-1.890.30331300.26952614X-RAY DIFFRACTION99.49
1.89-1.970.25561330.23542592X-RAY DIFFRACTION99.02
1.97-2.080.25651390.20812630X-RAY DIFFRACTION99.86
2.08-2.210.21651480.18452608X-RAY DIFFRACTION99.71
2.21-2.380.21651380.16722642X-RAY DIFFRACTION99.96
2.38-2.620.1991490.16432650X-RAY DIFFRACTION99.96
2.62-30.20441540.15322655X-RAY DIFFRACTION100
3-3.780.18581440.14182700X-RAY DIFFRACTION99.96
3.78-51.970.19571440.16342844X-RAY DIFFRACTION99.83
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)
13.95594065634-3.042958751352.130597048985.60058645866-2.83851653993.094972674010.05633418805730.178545740417-0.0853614455258-0.394408230075-0.01631376762570.07123213679410.3518692046210.0313112837043-0.006091718481870.186159388307-0.0418737994966-0.01198386777440.1520916578-0.03268446217780.1563943214459.40097366427-33.0055059157-17.8678419187
21.94657618328-1.846869079773.717142733853.05072354894-2.703130619767.7656972843-0.208019414125-0.150674590907-0.07367791143420.1068388025490.120177609593-0.01861998895450.119956498908-0.41601956152-0.01564550572990.135458503041-0.01852040372810.01579489229840.167491057516-0.03018953859940.215657793771.30999165882-25.5882698394-14.587635682
30.912205042648-0.777127427510.1334388232231.55482554355-0.05189461457070.4157385332390.0574307381890.08767332161210.06003794287020.0353986486432-0.0377652097520.0506536575298-0.11016920488-0.0180130380443-0.001662397641350.170134079214-0.0152770060569-0.002000400424360.1424682316560.006529273788760.14350245497513.5095107116-23.5315072855-11.0046789479
44.69645648116-1.13649930159-1.09419718272.803132271560.4300194539850.265416710206-0.05923151788180.0590928807654-0.07933748065420.19272296350.0224450100335-0.1121936725340.000446574245542-0.08515787684140.01607156994850.1400650271810.0135115785198-0.03400080148510.1461302243710.003580734705920.070930001565921.8313902965-22.7331540199-8.76099945818
51.63869634724-1.40116193251-0.834121299723.539945967912.659566576614.79818933789-0.187752802514-0.130047867855-0.00775255247630.2838462986250.1279715114790.1028783136140.387373355395-0.08027862350730.06875802514740.215815502705-0.00192049862225-0.006781022703610.1627544141460.0144098007670.13975167655124.7264332744-28.3925072643-5.60969099836
63.07367003342-0.940116223137-0.8929979330295.813575839280.5279998516245.09955079439-0.260939554127-0.421011216556-0.5566750554190.606850513938-0.090413020673-0.1449702664630.6628306708420.2564980424080.0240061173270.2232932867930.02771898561180.0005719650001860.1335120499950.05458014261510.20052099349823.0970982028-38.0855651956-5.64672792822
74.76902505199-0.379432084199-0.1655259906075.11729774342-0.4953538417775.349021671560.245087280029-0.5485839395370.05095255872270.3446218728060.09509711271650.136227305668-0.4178985033470.0415361693731-0.2832770349270.149885642332-0.07591052652260.02045238321660.1933996025020.002386309164660.1564575210510.36335073240.135607563344-8.3868071334
82.27409605388-1.370448277460.7546271508974.58777872924-2.628466384736.1794126667-0.0012336048773-0.1542439835390.1887672320370.160254964911-0.206319139553-0.499918141447-0.222105136460.2089234653720.1184072393630.116019776117-0.01680145566480.004658479086860.1745394739010.02234274041820.17070479721422.7638632892-9.19638879758-18.5749647047
97.28727363342-3.9782438724-1.843960891666.271670970011.066172684432.95488289830.167943583923-0.06269355763190.8136073567360.112134702651-0.234559992068-0.578376957201-0.52238764470.197975459685-0.000586938169620.210126755625-0.0700029496738-0.002340366601960.1338163340880.04973353186190.16506017364915.62629119753.30391188035-18.9671238309
100.5349101642250.6314361108260.5160257897870.933488093207-0.1056688520123.315533343310.06024478806530.0740966724010.521664229877-0.083474106741-0.200935629029-0.883973982509-0.1485378982680.249761342339-0.04686964326440.16473045288-0.02322178101340.02619295531660.1326023156030.05038597520670.27250710418718.28813517270.997852281932-11.6016388446
117.09084134907-2.764804494342.329246422094.72958447655-2.33001646091.48734871176-0.338976492103-0.2810706580780.2422475627160.4369622514140.196210154655-0.250162514162-0.2302936193040.02351212835840.1504995946010.319274044877-0.0141939286567-0.04496387471790.170425656469-0.0186453258670.14482807836317.3490442777-8.14103517407-2.06044652897
120.926496113034-0.6063356672520.007784299135551.92681705621-0.1892933396520.920221295211-0.0701964574324-0.08106429907420.01424249772640.1523807079990.1027376440050.09159635809780.1560924412360.0204549175406-0.007554464568840.130294687783-0.00847148406789-0.005453651161710.1417288714410.0006584654406350.12201555507111.5588568572-10.8524858016-12.5685208838
131.241131856140.0960928945541-1.004833262881.56298131101-0.1755938846725.06159377257-0.00785764047641-0.04484711790340.0251652702578-0.01523402468380.102049801940.1132948595110.05675199995650.0672967016909-0.03254204279140.109393466667-0.004659523361916.61109544094E-50.1037184291740.01416883871990.1269021157118.34265362146-10.0177876697-20.8014317049
140.521964939697-0.2736200515620.4746516659031.62532321334-0.433434310831.054072358260.0169062677099-0.08315638440170.02344579264980.117331133561-0.03702330793040.06376119657290.0115444405555-0.06489320650490.008485323645390.13057589706-0.00973317108061-0.00241489563460.14121720203-0.003687923830770.1599156043813.91260696325-8.91221134671-21.5207155755
155.710568746760.3174497708492.313828040831.90887390132-1.411439364428.8947694667-0.0448580328126-0.07631268265770.193952433488-0.1307884218890.1392066987590.204280386493-0.279892844024-0.280835285726-0.04061708301840.1596188425020.000161398368712-0.002007523676850.145994607564-0.003841344436630.1688410718843.752656732023.78625967258-20.6769449102
165.25417166042.21288084149-1.268744901856.21719980306-4.925380781073.973078800160.2495188132940.1669639883190.2131341119660.2601895527930.06078523503940.703707765375-0.156110395616-0.193627659394-0.2660157103030.2147846161440.02547977688810.01281878932560.140774944219-0.01675218939610.15809770438610.2449779112-33.1947103037-9.29263541714
174.24511841022-3.03690351378-0.1125517869314.6363475215-0.545870518922.392738763480.2221122612880.437762575748-0.280147782433-0.464009215558-0.2410544067210.2103074033140.2358185249920.08548504741480.02872176254650.1705566437550.0268046334922-0.003922170765520.2208433585270.007618001575860.16774142293316.6631628861-25.2388465889-23.3230206952
181.799143781480.982276255157-1.354225083624.04611047383-5.58517450117.84166030338-0.04870124009380.183911775855-0.171430042218-0.774148106567-0.177842749317-0.07786264227930.8938642114230.1836512396260.1540585188020.2613151210610.03685648972840.002168248418470.166504907632-0.009378770012450.18050631216518.8445512724-37.4667114418-16.7637050494
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 49 through 72 )BB49 - 7231 - 44
22chain 'B' and (resid 73 through 86 )BB73 - 8645 - 58
33chain 'B' and (resid 87 through 110 )BB87 - 11059 - 82
44chain 'B' and (resid 111 through 134 )BB111 - 13483 - 106
55chain 'B' and (resid 135 through 149 )BB135 - 149107 - 121
66chain 'B' and (resid 150 through 159 )BB150 - 159122 - 131
77chain 'A' and (resid 18 through 26 )AA18 - 261 - 9
88chain 'A' and (resid 27 through 35 )AA27 - 3510 - 18
99chain 'A' and (resid 36 through 48 )AA36 - 4819 - 31
1010chain 'A' and (resid 49 through 72 )AA49 - 7232 - 44
1111chain 'A' and (resid 73 through 86 )AA73 - 8645 - 58
1212chain 'A' and (resid 87 through 110 )AA87 - 11059 - 82
1313chain 'A' and (resid 111 through 128 )AA111 - 12883 - 100
1414chain 'A' and (resid 129 through 149 )AA129 - 149101 - 121
1515chain 'A' and (resid 150 through 160 )AA150 - 160122 - 132
1616chain 'B' and (resid 19 through 26 )BB19 - 261 - 8
1717chain 'B' and (resid 27 through 35 )BB27 - 359 - 17
1818chain 'B' and (resid 36 through 48 )BB36 - 4818 - 30

+
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