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- PDB-9eff: Crystal Structure of a nucleoid-associated protein (UBP) bound to... -

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Basic information

Entry
Database: PDB / ID: 9eff
TitleCrystal Structure of a nucleoid-associated protein (UBP) bound to DNA from Sulfolobus islandicus.
Components
  • Plasmid pARN4
  • ucm-1
  • ucm-2
KeywordsDNA BINDING PROTEIN / Sulfolobus islandicus / DNA replication protein / Archaea / nucleoid-associated protein
Function / homologyDNA / DNA (> 10) / Plasmid pARN4
Function and homology information
Biological speciesSulfolobus islandicus REY15A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsDhanaraju, R. / Gonzalez-Gutierrez, G. / Bell, S.D.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135178 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM152171 United States
Wellcome Trust086045/Z/08/Z United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: An archaeal nucleoid-associated protein binds an essential motif in DNA replication origins.
Authors: Dhanaraju, R. / Samson, R.Y. / Feng, X. / Costa, A. / Gonzalez-Gutierrez, G. / Bell, S.D.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmid pARN4
B: Plasmid pARN4
D: ucm-1
E: ucm-2
C: ucm-1
F: ucm-2


Theoretical massNumber of molelcules
Total (without water)42,2436
Polymers42,2436
Non-polymers00
Water6,593366
1
A: Plasmid pARN4
D: ucm-1
E: ucm-2


Theoretical massNumber of molelcules
Total (without water)21,1213
Polymers21,1213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint4 kcal/mol
Surface area7680 Å2
MethodPISA
2
B: Plasmid pARN4
C: ucm-1
F: ucm-2


Theoretical massNumber of molelcules
Total (without water)21,1213
Polymers21,1213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint3 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.742, 136.051, 38.380
Angle α, β, γ (deg.)90.000, 109.120, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Plasmid pARN4


Mass: 13541.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus REY15A (archaea) / Gene: SiRe_1573 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F0NFD3
#2: DNA chain ucm-1


Mass: 3808.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Sulfolobus islandicus REY15A (archaea)
#3: DNA chain ucm-2


Mass: 3772.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Sulfolobus islandicus REY15A (archaea)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Tris-HCl 0.05 M pH 8.0 - 8.5, Potassium Chloride 0.1 M, Magnesium Chloride 0.01 M and PEG400 26 - 30%
PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.91165 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 1.82→68.03 Å / Num. obs: 31882 / % possible obs: 98.4 % / Redundancy: 7 % / Biso Wilson estimate: 25.21 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.043 / Rrim(I) all: 0.115 / Rsym value: 0.106 / Net I/σ(I): 11.8
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1535 / CC1/2: 0.884 / Rpim(I) all: 0.416 / Rrim(I) all: 1.04 / Rsym value: 0.95 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→36.26 Å / SU ML: 0.2378 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2282 2694 4.58 %
Rwork0.2002 56075 -
obs0.2014 31170 91.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.27 Å2
Refinement stepCycle: LAST / Resolution: 1.82→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 972 0 366 3073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622869
X-RAY DIFFRACTIONf_angle_d1.15884070
X-RAY DIFFRACTIONf_chiral_restr0.0622429
X-RAY DIFFRACTIONf_plane_restr0.0091338
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.33351370.3022762X-RAY DIFFRACTION86.72
1.86-1.890.32141270.2962971X-RAY DIFFRACTION90.85
1.89-1.930.32071610.29192908X-RAY DIFFRACTION91.04
1.93-1.970.25161340.26492850X-RAY DIFFRACTION89.05
1.97-2.020.31111870.26922849X-RAY DIFFRACTION88.33
2.02-2.070.29511070.27862687X-RAY DIFFRACTION84.18
2.07-2.130.28631210.26052646X-RAY DIFFRACTION81.26
2.13-2.190.29921210.2452655X-RAY DIFFRACTION83.06
2.19-2.260.2691280.24332809X-RAY DIFFRACTION86.33
2.26-2.340.27981280.22822904X-RAY DIFFRACTION89.52
2.34-2.430.2691590.2223024X-RAY DIFFRACTION94.34
2.43-2.540.27581840.21413169X-RAY DIFFRACTION99.29
2.55-2.680.20291560.19433195X-RAY DIFFRACTION99.29
2.68-2.850.23041760.21733171X-RAY DIFFRACTION99.61
2.85-3.070.20691220.20073225X-RAY DIFFRACTION99.08
3.07-3.380.23411240.17673150X-RAY DIFFRACTION96.69
3.38-3.860.19061510.15753094X-RAY DIFFRACTION95.19
3.86-4.860.15761630.15732993X-RAY DIFFRACTION93.35
4.87-36.260.22021080.18043013X-RAY DIFFRACTION92.69
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)
16.577890426683.00563110065-2.994465035147.23110847889-3.510964184946.174141499550.403180923533-0.03000543263260.9537506649490.0743739773496-0.1343190086720.321523701253-1.01663270817-0.0683094967799-0.2798264651140.3670622254140.05308597807060.009234860410460.212480637063-0.04651033025820.290120057611-5.8066662414118.376628613712.387401345
24.76277242420.453060569534-0.2510774987814.47136416864-0.7508005242794.00399589050.0422294655682-0.2304321790990.04364077481410.2694284215380.06747843321570.00278586065902-0.106907613069-0.0325965713172-0.09464470707930.141945685257-0.000985121460105-0.008908354582530.110114065642-0.03023608020840.107772671405-3.696279292783.0268633808315.404769303
32.003055529382.00121042605-4.134432853242.0010319805-6.805505026922.00296352284-0.6636675860771.445268644731.48774493736-1.205281068211.175976605671.197216780260.166640798068-1.10124901275-0.3461454382320.329175935717-0.0710511280227-0.07074492098010.328645874060.0707762577730.363494649272-12.600578705810.89795919448.38146128997
42.045978475946.73716957521-3.52380806934.41411357963-3.930452485062.06602370681-0.3829915962170.2540491748010.409563500838-0.7177151502350.2305577211650.31238923767-0.6407898465230.1796880522490.3727814214490.568506681599-0.0357461446090.01767931709030.302743363854-0.01279373557450.5481809032642.7819138748219.21279151735.28252114739
52.67750438752-0.3353720688610.2051404318444.625241395833.750392049025.350923740620.1762336450150.136449397482-0.5654866855120.189979688115-0.124999495465-0.6432262278091.19867393180.1166879225720.05760226664730.6458219781260.04238564899340.1082835507790.2713958134370.07873129724350.487299542875-3.23896622939-33.071955817813.9600570083
66.940612996690.636971959551.443430969766.968081304231.66219775822.07151143563-0.195840972619-0.0811070773617-0.220250465540.07669227155480.0831857880943-0.02310266850780.316984865147-0.2658470205960.157025856520.269047670172-0.02494166148080.07987429554830.1563915780550.02086752373230.236193881037-7.65040163443-22.140682207311.1855447635
76.77680734676-0.6381658481331.505487714036.67508656346-0.4797962989475.26327920715-0.37137605698-0.1844945998930.03004569602920.301380533920.227434780798-0.4803655851920.05718875888760.3589326525760.1490139119050.189043403079-0.01179563755960.009794717546960.163993011698-0.01251012888370.223988205615-4.529982535-14.044890282217.3451111344
82.021908787152.060813502943.914767205081.59182457878-0.4713410428379.00736855713-0.0292002393180.418851409642-0.843266711583-0.2661196268360.127580247778-0.3458713482850.2308338782450.39943044179-0.09866864493520.721365325591-0.01000167102580.1710698497790.246015113439-0.1030042050950.584097661429-4.79092672408-33.58828061062.82795854105
94.20866191287-4.08920993972-2.450827395754.036011749832.801388924883.338961845450.111017352975-0.7745277842150.4223272437560.07303892292510.165063857118-0.0769212443250.1239703101540.403087063744-0.3269046667840.226458102217-0.0409388795814-0.002408933378950.31284253361-0.06011602268250.1413873719411.807505474698.1417777376821.7750377479
103.89195317430.72404268745-0.8930520420765.446897490192.225005756982.013667749430.03198023869510.58002195779-0.160270131713-0.2412353570420.417303233601-0.4323750892480.2046446217710.626797951537-0.4019776440270.189894297656-0.04060386599220.005936726525750.270960194274-0.02815671559480.1635207408458.92951253711-0.5413476612034.08443483248
115.49739693158-1.49376367950.1177589292674.146023075530.06993723718625.836412687690.1248084075060.3110850160530.0464273763394-0.378975067509-0.0015047535906-0.493128689744-0.305080055930.667323339582-0.136862490630.2027315747-0.0363943776232-0.01759326117820.264677279424-0.02028013967650.1282273190554.523307137623.744052504134.81014577075
124.20905605341-2.32418211689-1.064700839949.772670736925.140268107887.383304013090.0508423591787-0.2928808929760.2765489310740.8440963512390.141485087044-0.7392091690060.4044175329060.457961728927-0.1860841215290.216895212068-0.0787673332334-0.04359313949650.374887950953-0.04707384222120.2012660047325.701900051165.0980120406324.8737072349
133.04914650533-1.385038725050.6748469280494.90487478759-3.370294270164.44591785716-0.0496593486563-0.358228151997-0.04324323515070.2846637633440.01559455088740.1970726734020.255181317662-0.270647384497-0.06174082371310.298897965651-0.06244012816750.0734086084610.3177931341120.01595120369440.270736472648-15.1628230992-22.487159752216.066210107
147.475447117762.84455013296-7.456055635076.940097443030.1412659141359.02420719856-0.2198527732821.293021116690.775067550141-0.9797106516820.37826460290.0655366076572-0.651087357751-0.836359093837-0.1819802609840.576935496022-0.028237695673-0.04753575263230.3268686244760.03886286695170.193591149609-10.1079843782-13.6601920241-1.99458982883
154.185375037540.461447963132-0.3016831812883.434627094391.324417800134.18499297553-0.1979744319080.236469724674-0.0945047227912-0.3422246738030.08932753388270.1032865576760.510805393969-0.4308298115670.1313874831160.308359503166-0.05214438855580.0001652996179420.16044367442-0.02565798829450.190722228152-13.6059410058-18.85652190678.81590772184
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 30 )AA4 - 301 - 27
22chain 'A' and (resid 31 through 84 )AA31 - 8428 - 81
33chain 'A' and (resid 85 through 89 )AA85 - 8982 - 86
44chain 'A' and (resid 90 through 104 )AA90 - 10487 - 101
55chain 'B' and (resid 4 through 30 )BB4 - 301 - 27
66chain 'B' and (resid 31 through 57 )BB31 - 5728 - 54
77chain 'B' and (resid 58 through 89 )BB58 - 8955 - 86
88chain 'B' and (resid 90 through 105 )BB90 - 10587 - 102
99chain 'D' and (resid 20 through 26 )DC20 - 26
1010chain 'D' and (resid 27 through 31 )DC27 - 31
1111chain 'D' and (resid 41 through 46 )DC41 - 46
1212chain 'D' and (resid 47 through 52 )DC47 - 52
1313chain 'C' and (resid 20 through 26 )CD20 - 26
1414chain 'C' and (resid 27 through 31 )CD27 - 31
1515chain 'C' and (resid 41 through 52 )CD41 - 52

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