[English] 日本語
Yorodumi
- PDB-5zj5: Guanine-specific ADP-ribosyltransferase with NADH and GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zj5
TitleGuanine-specific ADP-ribosyltransferase with NADH and GDP
ComponentsADP-ribosyltransferasePoly (ADP-ribose) polymerase
KeywordsTRANSFERASE / ADP-ribosyltransferase / TOXIN
Function / homologyglycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / extracellular region / GUANOSINE-5'-DIPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Guanine-specific ADP-ribosyl transferase
Function and homology information
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56811199264 Å
AuthorsYoshida, T. / Tsuge, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K15095 Japan
Japan Society for the Promotion of Science15K08289 Japan
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Substrate N2atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP.
Authors: Yoshida, T. / Tsuge, H.
History
DepositionMar 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 2023Group: 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: ADP-ribosyltransferase
B: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6735
Polymers36,8992
Non-polymers1,7743
Water4,053225
1
A: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5583
Polymers18,4491
Non-polymers1,1092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1152
Polymers18,4491
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-26 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.197, 40.049, 77.054
Angle α, β, γ (deg.)90.000, 113.967, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein ADP-ribosyltransferase / Poly (ADP-ribose) polymerase / ScARP


Mass: 18449.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO5461 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: Q9L1E4
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: ammonium acetate, PEG 10000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.568→27.15 Å / Num. obs: 45603 / % possible obs: 99.57 % / Redundancy: 5.5 % / Biso Wilson estimate: 16.5655514862 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.02819 / Rrim(I) all: 0.06696 / Net I/σ(I): 24.54
Reflection shellResolution: 1.568→1.624 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.53 / Num. unique obs: 4374 / CC1/2: 0.896 / Rpim(I) all: 0.1828 / Rrim(I) all: 0.4217 / % possible all: 96.58

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAZ

5daz


Resolution: 1.56811199264→27.1493266712 Å / SU ML: 0.147343210589 / Cross valid method: FREE R-VALUE / σ(F): 1.3473636464 / Phase error: 19.4471045058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.208409667716 2000 4.38577255384 %
Rwork0.173661767563 43602 -
obs0.1751746266 45602 99.5937800297 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.9712093339 Å2
Refinement stepCycle: LAST / Resolution: 1.56811199264→27.1493266712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 116 225 2880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01250228312772769
X-RAY DIFFRACTIONf_angle_d1.444445826373803
X-RAY DIFFRACTIONf_chiral_restr0.0804886266371388
X-RAY DIFFRACTIONf_plane_restr0.00979572384894486
X-RAY DIFFRACTIONf_dihedral_angle_d12.38266690741898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5681-1.60730.2213261434471370.1920763226472981X-RAY DIFFRACTION95.322531336
1.6073-1.65080.1922681877881390.1762707314193044X-RAY DIFFRACTION99.8744901161
1.6508-1.69930.2195693506241440.170372850923133X-RAY DIFFRACTION100
1.6993-1.75420.2137562937051420.1764563532593100X-RAY DIFFRACTION99.969164354
1.7542-1.81690.1935674760481430.1670407984193115X-RAY DIFFRACTION100
1.8169-1.88960.2230290199981420.1674798218493088X-RAY DIFFRACTION99.9690498298
1.8896-1.97560.2207364864631420.1658676251983109X-RAY DIFFRACTION100
1.9756-2.07970.2228402475721430.1777502554163107X-RAY DIFFRACTION100
2.0797-2.20990.2284075890391440.1808602154363132X-RAY DIFFRACTION100
2.2099-2.38050.2110329216571420.1762094215693111X-RAY DIFFRACTION99.9078624079
2.3805-2.61990.2331329051111440.1885657637423138X-RAY DIFFRACTION100
2.6199-2.99850.2038990838941440.1929680342933147X-RAY DIFFRACTION99.9089253188
2.9985-3.77620.2060921037181450.1801856816633152X-RAY DIFFRACTION99.8788245986
3.7762-27.15340.183787547191490.1491174476243245X-RAY DIFFRACTION99.5016124304
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)
13.20971616818-4.16881536296-4.341882607427.263726704373.928457058567.580734052350.052279070890.403551228021-0.855999830332-0.392618335381-0.09599222764410.415888074590.562794946214-0.3726269055890.002968217664780.343721541914-0.0696331182018-0.109751859160.238322575993-0.01084895373880.329092915172-123.83675434210.734927933916.9194104418
22.1841505106-0.2326830681061.284730805522.227699595670.2462111292032.718070476370.09608207692660.0576295100025-0.317625458142-0.00759378710613-0.02836387324950.4455726952630.203207729791-0.394742198802-0.1010542263080.146447979713-0.0275511793667-0.005685443455860.184837578145-0.005446915242460.23408257777-128.17371024119.391186026115.0551347398
34.5064270878-1.63852505272-1.152099771366.511726432741.032678820835.21028485832-0.0391589316429-0.2088770463070.07655923215350.4875057818710.04579104826670.124279316798-0.277048925394-0.335782625164-0.02767729421630.1055548276520.0214328958001-0.01494000778690.0936956696432-0.01592573512560.117639616727-119.1161793127.819626472330.513932371
43.43594374955-1.729013927663.987889454231.01514172016-1.888236865134.767663727890.0604879562817-0.143839958045-0.3117826835780.09350711457380.2362638413010.51933294459-0.17788975478-0.716228475263-0.2624566074910.1576175110780.05733249432930.03096020917130.3168822733510.02670915342480.282883015759-133.05641362128.198329344321.1518260186
55.07535565563-2.940541261062.181036994594.16983372006-1.702698716971.025557156520.0449658899060.05823410086050.011526700312-0.0185421442294-0.006042019572530.254617003019-0.183107643779-0.347815652511-0.04140341586570.1303806658560.0703100470718-0.004090239319550.195750436318-0.02049457515010.134315493064-127.66917763731.755334321915.1999210578
61.196758610760.4052056241470.4884709107140.462073192756-0.5197119604641.288056754080.03416999362720.01111163887640.07549701484180.158840057723-0.008955635789270.0551519461957-0.153267735472-0.0437506188218-0.02398287293920.1330542821430.0232206802170.008450846394910.0687909471674-0.005899768020960.120864714233-114.24402559729.649203167621.553591784
71.46463907906-0.1566397166950.8831669411580.731443314986-0.4808357454543.66297534204-0.008336484928850.0885051599783-0.01253951247720.01610740129520.05187079739730.0895475193472-0.146011864159-0.285161809093-0.04161623135360.1131279307180.03753654739510.01837996123330.0905616778528-0.006153997780110.129260953078-119.81826207227.319128794116.3083445121
81.79423447744-1.977368827760.2445653034235.04655294416-1.803109705910.91988827419-0.0236475835387-0.01429576796290.229283275850.03508352640760.0379959477548-0.0428917149181-0.4215168280220.133196123645-0.030018078250.226558229943-0.00785882424119-0.02656780057010.0943094269244-0.01669921854290.159659192937-105.63304338336.350467808228.9940399004
93.328049792850.05411508598910.9901624046370.488254842123-1.065309201644.905010775040.117147554597-0.0883566865879-0.09832049169120.132985542731-0.02754359490940.1923742022190.29410305496-0.251437511249-0.0980597548680.1366281082670.01912664286930.01575605614930.06240492475130.008373125536730.142648429012-114.60228039816.545475034830.605667103
106.263018605150.97558613978-5.255573707012.490224682021.168402374366.19981264396-0.01703376980780.5853303642420.53577599093-0.0862153753461-0.136206882514-0.362206231399-0.810221069560.933562280388-0.2770168292630.285195124209-0.06819245385050.05491315118270.463407394410.1035088674680.249675731975-86.354270435533.74972036729.73082705478
112.27063236431-0.429464683609-0.8593347634520.8573086266240.4059242524892.06263082090.07715578351960.3637150822880.00243336675242-0.11167788302-0.0835288568825-0.1392190544020.1764240158070.4459859319690.01351745449430.1653308930680.07804360910890.007630141193790.2749099860120.008901718652740.145425903897-88.718786485622.018142439413.9614101894
122.090705261310.294793282316-0.2647674363160.63351601542-0.0886481086223.27282069060.03856500599030.172615449308-0.059649090801-0.0556179056116-0.0197134070893-0.03412033558150.1841105505010.1485190797470.007623296931660.1183036007810.044487212511-0.006960317757930.08334816030220.000714228341630.112225658054-97.970462111623.18263392419.48941031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 93 )
4X-RAY DIFFRACTION4chain 'A' and (resid 94 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 148 )
7X-RAY DIFFRACTION7chain 'A' and (resid 149 through 181 )
8X-RAY DIFFRACTION8chain 'A' and (resid 182 through 193 )
9X-RAY DIFFRACTION9chain 'A' and (resid 194 through 204 )
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 65 )
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 123 )
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 204 )

+
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