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- PDB-8ubs: Crystal structure of NrdJ-1 split intein fusion -

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Basic information

Entry
Database: PDB / ID: 8ubs
TitleCrystal structure of NrdJ-1 split intein fusion
ComponentsNrdJ-1
KeywordsSPLICING / Fusion of the split intein NrdJ-1.
Function / homologyFORMIC ACID
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKofoed, C. / Ye, X. / Jeffrey, P.D. / Muir, T.W.
Funding support United States, European Union, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM086868-25 United States
European Molecular Biology Organization (EMBO)EMBO ALTF 1189-2020European Union
CitationJournal: Nature / Year: 2025
Title: Programmable protein ligation on cell surfaces.
Authors: Kofoed, C. / Erkalo, G. / Tay, N.E.S. / Ye, X. / Lin, Y. / Muir, T.W.
History
DepositionSep 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: 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.title / _citation.year
Revision 1.2Aug 13, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 1, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NrdJ-1
B: NrdJ-1
C: NrdJ-1
D: NrdJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,21619
Polymers67,7564
Non-polymers46015
Water7,170398
1
A: NrdJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1238
Polymers16,9391
Non-polymers1847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NrdJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1235
Polymers16,9391
Non-polymers1844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NrdJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9853
Polymers16,9391
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NrdJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9853
Polymers16,9391
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.793, 84.383, 174.709
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

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Components

#1: Protein
NrdJ-1


Mass: 16938.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Catalytically inactive fusion of split intein NrdJ-1 N and C fragments carrying C1A and N145A mutations.
Source: (gene. exp.) marine metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4.5 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 5, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.95→29.12 Å / Num. obs: 53184 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.053 / Rrim(I) all: 0.139 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3754 / CC1/2: 0.808 / Rpim(I) all: 0.352 / Rrim(I) all: 0.916 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.12 Å / SU ML: 0.2097 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.3388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 2665 5.02 %
Rwork0.1801 50434 -
obs0.1822 53099 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.26 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4724 0 25 398 5147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644889
X-RAY DIFFRACTIONf_angle_d0.80156656
X-RAY DIFFRACTIONf_chiral_restr0.0608797
X-RAY DIFFRACTIONf_plane_restr0.0043858
X-RAY DIFFRACTIONf_dihedral_angle_d21.42511812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.27311360.22792502X-RAY DIFFRACTION97.24
1.99-2.030.26861180.21722649X-RAY DIFFRACTION100
2.03-2.070.23071480.20692608X-RAY DIFFRACTION100
2.07-2.110.24681280.19192664X-RAY DIFFRACTION100
2.11-2.160.28841430.18312587X-RAY DIFFRACTION99.96
2.16-2.220.22541300.1772659X-RAY DIFFRACTION100
2.22-2.280.19651420.17412592X-RAY DIFFRACTION100
2.28-2.340.20091480.17032639X-RAY DIFFRACTION99.96
2.34-2.420.26111330.18372631X-RAY DIFFRACTION99.96
2.42-2.510.25811400.19022635X-RAY DIFFRACTION99.96
2.51-2.610.24861240.20892656X-RAY DIFFRACTION100
2.61-2.730.21951320.20052693X-RAY DIFFRACTION100
2.73-2.870.28221420.21442656X-RAY DIFFRACTION99.96
2.87-3.050.25141320.20162659X-RAY DIFFRACTION100
3.05-3.280.23381510.18382650X-RAY DIFFRACTION100
3.28-3.610.19411500.15662669X-RAY DIFFRACTION100
3.61-4.130.16111550.14332701X-RAY DIFFRACTION100
4.14-5.20.17641430.13142733X-RAY DIFFRACTION100
5.2-29.120.24711700.22212851X-RAY DIFFRACTION99.44
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)
17.1352330604-3.24161076175.495031294886.6846754025-2.751739185358.086462604030.226343832462-0.0788781213424-0.235122953283-0.069895754753-0.04376842503460.08055043135630.552295018733-0.00778787001033-0.09857764717230.1796934836180.0146578405497-0.002544624984550.127611514045-0.02040296423480.2018463438533.41445159586-7.675898916723.19972062806
24.67498489934-1.066682169181.539599344295.560196641021.635449241525.46432139634-0.168895668768-0.01132679470350.1655176600070.3062918593580.208842302828-0.272456439044-0.01973560356310.325273180025-0.1266153502230.162343494366-0.0073066829994-0.06489890286490.1278607648050.01254033951840.19034654501610.0961674593-6.185141507883.40190491986
33.74663401723-1.381954747750.3834410924655.184722114171.739077868472.68702117012-0.09059378927260.114299928626-0.02186859633320.02844161273410.01614457087940.4528780167960.0148809521631-0.1894221206440.07272490761560.147077348213-0.01228619983660.01227843220570.1962747285260.02768679514280.203246352533-3.9880333258-5.853260885-8.30084810902
47.71567645502-4.65751388039-2.48766826467.922641679324.182853526218.470671120540.1339356272650.463543168679-0.0106401669502-0.3256690755830.0111425717619-0.06073286029440.23498235645-0.171075440973-0.159776394580.151070076744-0.0652067213048-0.01320356885320.1905348179180.0366142188530.163006633354.90534138534-5.10072261547-16.6694318259
54.720400776980.2662354649030.8128738350822.111781323063.347050931885.33705697990.29862818293-0.264864896085-0.6330165402320.917501949154-0.0173721762014-0.115949942861.085251208250.0437162628345-0.2420381803150.412530846044-0.0508385595753-0.06154828847430.2308450649450.02748847816570.2309900730887.13572026512-18.12933171-4.97441582539
62.60045359381-1.814006242270.3059277918792.43672762710.3249942139022.23903948338-0.1038607176490.01357370804050.06415918334360.1447210222020.0792634270842-0.0248964159854-0.003529358409550.04885888732780.007872021325610.156039842496-0.0531150362001-0.01760896359270.1419269103340.03592686595610.1643070001223.32586140932-5.46159420437-6.88635369251
73.95064675145-1.667701697921.073844341495.852170295830.6647316194433.83866297141-0.04290100261450.01490354347320.617267952055-0.260283255524-0.01140574449620.175342796162-0.89342779178-0.4921219200210.03732259977680.4560649223670.105614482002-0.02279290928220.2378501795240.02660652561520.33777313635219.797615122723.7476604488-15.9509446232
83.184789569230.09187019108430.5553082140262.852144773010.5333782645143.12016464279-0.008417287308480.04204466774140.168865704986-0.01146694788370.0402249841492-0.0280015390695-0.311426505044-0.136964153347-0.03178451618520.166948506380.0183490727659-0.0003799248919720.1265826518610.03532733800780.16362526753321.30879341059.55460713463-16.6779197539
96.080999423491.856575045481.389342345136.238755047971.494194036818.98569087527-0.4871938705750.858017113645-0.28757904741-0.5795638036640.0775091076122-0.0452487724686-0.07871037481610.7346216679350.3269311267950.263097555448-0.04424132933750.04842899282220.426306353810.02414666376050.23039629196931.5079818151-8.3216181861714.1230587921
103.704759089730.656349657740.575560833082.25345112566-0.4199980942113.53860695506-0.3730636424650.8158237140250.243548826458-0.4182967799340.173987514572-0.121163468865-0.4233374993760.5497184535270.1579752546140.316863885352-0.104977370804-0.01333962939540.3942527176760.03427467374280.19058599752725.6954412253-5.8084221543711.044717434
115.881071238392.25835746270.6728061064594.67696159178-1.230261290554.92632806519-0.1764841227530.211301425662-0.300827300628-0.1930409330010.00205391605811-0.3942635268310.08278395895190.4874045475640.09300017754650.1543699320450.02993492715510.02104274348510.2887854207540.04345941424020.19307015186934.6599362733-7.2843918499127.5579476475
124.972158737370.776355175391.313553283712.575129522280.7440357711614.28834067003-0.157148141203-0.1278945578530.2297596204310.049863945470.0048697165583-0.0962458175346-0.154461853730.1283662204870.2450310892760.153155913294-0.0100494880226-0.01538472825930.1812712878130.008417440080720.15550511676627.1640717062-3.8807637254329.3105307351
134.714256550371.348272402952.257871053594.299836165853.932122816817.531997247380.0559068350486-0.199154147984-0.3781979387130.0964088881457-0.2573115263510.1783938088250.631895450226-0.3311647488740.06547818018630.219121813658-0.01287341472090.02186127423160.1468865090030.03723632567120.22293754615922.6264633638-14.454197589927.224107477
145.08105447231.261974725381.854815178011.090304991350.9548018116723.99346215407-0.2806162494390.3645689329320.157654660793-0.1543008419250.0513819351898-0.0811030879757-0.1973179443820.4141283631110.1847955976950.180586306523-0.01035996464880.004698548618250.1936668362870.03139480854710.17785899830929.4788989885-4.9462701170323.1405589537
156.557000100642.550494449991.096045969417.802027539841.378052953397.65039157446-0.3045860943-0.3714597999721.449863893850.3369081639960.06229099041610.36829128274-1.095479028970.1496538723950.211055043160.431260201168-0.0300207066006-0.07610086798080.274630964142-0.05505201327050.57695446191110.78620081915.567345712841.5138372942
165.73098445456-1.000239144061.190866024753.5871532309-5.841909616129.773547908440.123833399318-0.3513759625910.967916446944-0.155729802491-0.352419243212-0.197941223535-0.1457230748340.8774819507970.281517833360.370427184751-0.122561530722-0.05304150467360.501696419237-0.1740772768270.5378115797820.921627633910.852692942643.6444183699
173.394983749530.3558196598652.229883238253.67115104787-1.335481063312.14148782504-0.181691994272-0.004891477029750.472029139334-0.0231703729331-0.01157583626040.109279773489-0.309398319455-0.3738287123330.1394800158380.184489130283-0.00814843635799-0.009306454604210.250117782157-0.005772099506270.2635907980193.405392184311.7259741736941.434036914
182.61652650941-2.469935741122.868099900459.36366882955-3.874804603779.09428459728-0.04009869805580.121663414896-0.2324982697480.1496622956860.03833808234920.02267005292280.1677928696270.3521231694610.06237153742850.145850855384-0.0110125644460.02664648451570.257691260809-0.002913029230340.15329205558212.1371688589-6.7266362897840.5469930399
193.885767459940.1341462323042.778690847531.95615317597-1.90474869725.56179512768-0.0242983566751-0.777268966760.3172132460190.388394257517-0.0914367617332-0.0845429623518-0.5855725617660.04340740688010.1628839067920.251837872595-0.01693373313170.02120617175990.442872304223-0.09704826969360.186315123388.43080829761-1.3036802704149.6028250272
205.8887964722-0.4394130731184.138462584022.44393541004-0.4715741633494.85185904091-0.2207669489810.1660741684710.857689956048-0.134280210380.0465609513346-0.129965421313-0.2972049538740.3309531482260.1767641014770.271522949878-0.04726161195950.007723699596960.212177602888-0.01588101405480.30792004401713.29291900456.5119085217938.1899075519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 151 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 56 )
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 151 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 16 )
10X-RAY DIFFRACTION10chain 'C' and (resid 17 through 56 )
11X-RAY DIFFRACTION11chain 'C' and (resid 57 through 74 )
12X-RAY DIFFRACTION12chain 'C' and (resid 75 through 97 )
13X-RAY DIFFRACTION13chain 'C' and (resid 98 through 113 )
14X-RAY DIFFRACTION14chain 'C' and (resid 114 through 151 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 29 )
16X-RAY DIFFRACTION16chain 'D' and (resid 30 through 56 )
17X-RAY DIFFRACTION17chain 'D' and (resid 57 through 79 )
18X-RAY DIFFRACTION18chain 'D' and (resid 80 through 103 )
19X-RAY DIFFRACTION19chain 'D' and (resid 104 through 124 )
20X-RAY DIFFRACTION20chain 'D' and (resid 125 through 151 )

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