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- PDB-5zj5: Guanine-specific ADP-ribosyltransferase with NADH and GDP -

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Basic information

Entry
Database: PDB / ID: 5zj5
TitleGuanine-specific ADP-ribosyltransferase with NADH and GDP
ComponentsADP-ribosyltransferase
KeywordsTRANSFERASE / ADP-ribosyltransferase / TOXIN
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / extracellular region
Similarity search - Function
GUANOSINE-5'-DIPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Guanine-specific ADP-ribosyl transferase
Similarity search - Component
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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

#1: Protein ADP-ribosyltransferase / 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


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


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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 )

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