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Basic information

Entry
Database: PDB / ID: 9qth
TitleInquilinus NrnC
ComponentsInquilinus NrnC
KeywordsHYDROLASE / nuclease / NrnC
Biological speciesInquilinus limosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMortensen, S. / Burnim, A. / Dufault-Thompson, K. / Jiang, X. / Lipka, A.E. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 AI142400 United States
CitationJournal: Sci Adv / Year: 2026
Title: Ancestral proteins trace the emergence of substrate specificity and oligomerization within bacterial DEDDy dinucleases.
Authors: Mortensen, S. / Burnim, A.A. / Dufault-Thompson, K. / Lipka, A.E. / Jiang, X. / Sondermann, H.
History
DepositionApr 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inquilinus NrnC
B: Inquilinus NrnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2868
Polymers45,1182
Non-polymers1686
Water10,737596
1
A: Inquilinus NrnC
B: Inquilinus NrnC
hetero molecules

A: Inquilinus NrnC
B: Inquilinus NrnC
hetero molecules

A: Inquilinus NrnC
B: Inquilinus NrnC
hetero molecules

A: Inquilinus NrnC
B: Inquilinus NrnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,14332
Polymers180,4708
Non-polymers67324
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Unit cell
Length a, b, c (Å)120.708, 120.708, 71.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 2 through 35 or resid 37...
d_2ens_1(chain "B" and (resid 2 through 35 or resid 37...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERASPASPAA2 - 352 - 35
d_12LEULEULYSLYSAA37 - 7537 - 75
d_13PHEPHESERSERAA77 - 13077 - 130
d_14GLNGLNHISHISAA132 - 204132 - 204
d_21SERSERASPASPBB2 - 352 - 35
d_22LEULEULYSLYSBB37 - 7537 - 75
d_23PHEPHESERSERBB77 - 13077 - 130
d_24GLNGLNHISHISBB132 - 204132 - 204

NCS oper: (Code: givenMatrix: (0.645680942607, -0.763605830899, 0.00150178904061), (-0.763605837837, -0.645682309856, -0.000692214331598), (0.0014982575165, -0.000699825276496, -0.999998632734)Vector: ...NCS oper: (Code: given
Matrix: (0.645680942607, -0.763605830899, 0.00150178904061), (-0.763605837837, -0.645682309856, -0.000692214331598), (0.0014982575165, -0.000699825276496, -0.999998632734)
Vector: -21.3573290684, -46.0105424492, 59.8634450851)

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Components

#1: Protein Inquilinus NrnC


Mass: 22558.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Inquilinus limosus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris (pH 5.5), 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→46.19 Å / Num. obs: 49513 / % possible obs: 99.8 % / Redundancy: 18.4 % / Biso Wilson estimate: 19.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1793 / Net I/σ(I): 19.75
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 18.9 % / Rmerge(I) obs: 2.332 / Num. unique obs: 4828 / CC1/2: 0.793 / % possible all: 99.73

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.19 Å / SU ML: 0.1791 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.9724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1991 1495 1.59 %
Rwork0.1766 92258 -
obs0.1769 49496 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 6 596 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063225
X-RAY DIFFRACTIONf_angle_d0.89254379
X-RAY DIFFRACTIONf_chiral_restr0.0512503
X-RAY DIFFRACTIONf_plane_restr0.0073571
X-RAY DIFFRACTIONf_dihedral_angle_d12.48251191
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.443199777561 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.34781330.35568345X-RAY DIFFRACTION99.78
1.86-1.920.24671360.2558403X-RAY DIFFRACTION99.85
1.92-20.24191340.20378357X-RAY DIFFRACTION99.92
2-2.090.20681420.18368386X-RAY DIFFRACTION99.96
2.09-2.20.22781370.17268426X-RAY DIFFRACTION99.86
2.2-2.340.18731360.16528375X-RAY DIFFRACTION100
2.34-2.520.2181350.18088400X-RAY DIFFRACTION100
2.52-2.780.22831390.17748398X-RAY DIFFRACTION100
2.78-3.180.20651330.18038424X-RAY DIFFRACTION99.96
3.18-40.17091340.1548351X-RAY DIFFRACTION99.47
4-46.190.1531360.14938393X-RAY DIFFRACTION99.73
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)
13.271538796131.371632777720.3195367280934.901822312250.7720090418623.665838659530.03074181178250.09267563479920.0470876266712-0.09887515763180.0585805425428-0.1569076102380.1960335544620.0617030679539-0.06523918476410.1039865843910.03292117517230.04229467450760.140245842731-0.0117818713760.12100001877-34.8843848117-31.46109362674.48628419631
23.574095664790.0153904633283-0.6333294816632.094686930250.5725676208972.19440418743-0.01118110514390.00125188053495-0.0824951955946-0.00630577416090.003600128217350.008834334737680.0913610566732-0.2016259574150.01534593922290.069328783354-0.0001422575119850.001435311593940.0843058255664-0.007234984461180.0801853510912-41.8454291022-28.299443522512.6603785415
30.6177773620730.653285762906-0.02733325431162.89884635045-0.1147711249371.2208874440.0451614490743-0.004990227575620.0754695704174-0.114966346967-0.04136242325520.128736054131-0.144650136339-0.0666389339103-0.009335515037350.09457241421540.02234244824290.001800495614010.0912534713115-0.002633473255810.0859513653694-37.5159706807-14.068097588915.3650126683
45.643543229634.45048138341-1.488373122153.52438632533-1.435326398593.05632681733-0.05385481698540.2525801001620.372429417301-0.2388678285340.09488375444490.379933265558-0.0541806821055-0.431580325747-0.0349934682030.1561075392860.0526809276872-0.01525082801320.207556210862-0.005816951438440.158544510471-47.9776749002-20.44313103993.53100369289
50.307196388791-0.0300099330337-0.1082661561241.22054607364-0.02466534872662.13916317216-0.0453174109802-0.003588013474880.0145022959929-0.00107565491012-0.0158414211846-0.114570163228-0.0258599898723-0.1297757250710.03683962961390.1043416963360.00760935501213-0.01110222793880.113586616095-0.01568251011360.110784143017-34.1173653446-10.958429405422.2593318553
61.32496247099-0.3075459390160.6565123555475.813860588031.129903363771.32908617799-0.0998939785201-0.243143221512-0.1151657009050.9817705019190.274821166545-0.6722018826360.1257151453020.2745995231220.101140031920.2797484935560.0488435311489-0.150914443690.2160728516070.0002135876958980.323591870919-19.82756666470.86603959877655.3671621355
72.79550593031-1.121010579250.597617972424.121913791050.2805959845281.840045758420.0185717949262-0.0286842812820.1098093351050.1359832521270.0471169396329-0.238205064766-0.1834868144380.0295021595808-0.014109872620.134047908659-0.0138591283392-0.02202814439510.100401193304-0.01296331583250.100079890766-26.6637486424.0112026766847.1955077483
81.411224873141.46032968805-0.2592935029023.04736623748-0.2109608958111.43523866357-0.000750727578133-0.0817511441710.05424179323370.0376792635644-0.001565636917540.110548772733-0.0502229664373-0.0943441983656-0.0210569036460.1056947047260.0264007286385-0.01723968866640.09260148956480.0001314183173930.0825327529687-34.7376391388-8.3477120004244.4739827792
90.123802728885-0.125529140509-0.3691457018328.23787032015-2.499209120682.094199185880.0452674597236-0.1304197676210.08159075045240.5034102073780.04797798411360.605563993809-0.169833797849-0.0472325361026-0.1132562146940.2369275002220.01888292218170.005669992446530.185479501167-0.02910699411050.165684089987-36.6891142633.8547340508256.2890139173
100.3608039403480.09157859416650.08894229846811.09801884496-0.3090896370611.85538964395-0.05927000526770.00992045665703-0.0760994524098-0.003981850020570.0293863906626-0.0404581344651-0.132231977995-0.07149131292460.02042415403730.1189886669430.0149680500547-0.003453985978820.129941004199-0.008703982136730.136278147097-35.0068489607-12.875642703237.5857690676
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 19 )AA2 - 191 - 18
22chain 'A' and (resid 20 through 69 )AA20 - 6919 - 68
33chain 'A' and (resid 70 through 125 )AA70 - 12569 - 124
44chain 'A' and (resid 126 through 157 )AA126 - 157125 - 156
55chain 'A' and (resid 158 through 204 )AA158 - 204157 - 203
66chain 'B' and (resid 2 through 19 )BB2 - 191 - 18
77chain 'B' and (resid 20 through 69 )BB20 - 6919 - 68
88chain 'B' and (resid 70 through 125 )BB70 - 12569 - 124
99chain 'B' and (resid 126 through 157 )BB126 - 157125 - 156
1010chain 'B' and (resid 158 through 204 )BB158 - 204157 - 203

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