[English] 日本語
Yorodumi
- PDB-9efd: Crystal Structure in space group C2221 of a nucleoid-associated p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9efd
TitleCrystal Structure in space group C2221 of a nucleoid-associated protein (UBP) from Sulfolobus islandicus.
ComponentsPlasmid pARN4
KeywordsDNA BINDING PROTEIN / Sulfolobus islandicus / Archaea / DNA sequence specific binding protein / nucleoid-associated protein / DNA replication origin binding protein / DNA Major groove binding protein
Function / homologyDI(HYDROXYETHYL)ETHER / Plasmid pARN4
Function and homology information
Biological speciesSulfolobus islandicus REY15A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasmid pARN4
B: Plasmid pARN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3824
Polymers27,0822
Non-polymers3002
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-17 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.010, 159.670, 47.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2 M LiCl NaAc 0.1 M pH=5 PEG6000 18-24%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24984 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24984 Å / Relative weight: 1
ReflectionResolution: 2.73→47.31 Å / Num. obs: 9913 / % possible obs: 99.6 % / Redundancy: 13.8 % / Biso Wilson estimate: 61.94 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Rrim(I) all: 0.119 / Rsym value: 0.115 / Net I/σ(I): 22.6
Reflection shellResolution: 2.73→2.86 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1279 / CC1/2: 0.894 / Rpim(I) all: 0.557 / Rrim(I) all: 1.986 / Rsym value: 1.94 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→46.43 Å / SU ML: 0.325 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.5915
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2779 423 4.34 %
Rwork0.2675 9316 -
obs0.2679 9739 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.56 Å2
Refinement stepCycle: LAST / Resolution: 2.74→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 20 27 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251806
X-RAY DIFFRACTIONf_angle_d0.46172425
X-RAY DIFFRACTIONf_chiral_restr0.0446255
X-RAY DIFFRACTIONf_plane_restr0.0082289
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-3.130.42461390.37512967X-RAY DIFFRACTION96.52
3.13-3.950.28471380.27763117X-RAY DIFFRACTION99.66
3.95-46.430.24361460.23913232X-RAY DIFFRACTION99.53
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)
17.791652294441.96579252441-7.497126726735.8859948931-1.756703321952.165422779240.1481941949290.4920569940810.6520709222380.487023766350.640833254796-0.9956176254290.0518484574326-0.458504263298-0.5480465920580.6724867292090.162332520789-0.2392953378240.63249163974-0.1055362687080.5750613617247.102829400528.16670775817.96008230935
29.79502989934-7.23846639074-0.5502590367069.25283861184-0.03529308873060.662735527845-0.595586073569-1.087733472560.1804507655690.09499571228110.961859652691-0.54379201766-0.5725619085-1.66423192257-0.2775275820370.7193912711520.248170366025-0.04482251539030.7309518890990.003724405301870.21297756639729.894834028836.28508515947.60306290995
34.420614940.02898497405745.351321248237.37545102085-6.212415243217.668751608750.3327418081380.274095130037-0.480403866441-0.501576710159-0.0951049004609-0.1678505025790.30249609834-0.0286252204091-0.2492024310850.6248862248090.1236813489190.01338559636460.720809603561-0.02867898354370.21052965579529.804960978831.7172726939-3.51993346168
48.21910078949-2.571264515792.587934985636.07837248438-2.43492782238.376976573781.55192959788-2.149841107780.255694565694-0.221220723697-1.208966540541.292151656220.936409875431-1.72626580342-0.3997667373990.603586101533-0.09339394240350.04461969012541.40796878064-0.08991708401160.76034869168114.267919412330.8309926742-9.19989094078
58.357797658-1.575889209296.266422128256.561518018720.1032873217714.51795417853-0.381722256710.7824768453190.64262274298-0.148594771173-0.249302721356-0.349671571636-0.4642497295180.4054328461360.5541947792890.816833473460.05919010980360.009418384148830.5415207694880.05480445325570.27187883810228.597490465942.7119823363-7.84422682872
61.68991693921-0.160000955451-1.163694567029.95561326813-0.9888932710061.874433804690.1358162986310.411006836819-1.00888426639-0.0932282704435-0.04146224828040.176661293090.6480850769560.0659896659848-0.02131718597190.444023390737-0.0118650244955-0.1980779777740.52577007035-0.054773791490.86747008785641.183975965711.48546740318.13539954258
73.09073095047-1.34189005643-2.31673903671.83610841041-1.394798258595.82466598209-0.09653816738470.60837463934-0.6274252262560.05285617072560.1197792238670.3941696081340.826881348211-1.37532262645-0.06696844620410.908177743257-0.231118390971-0.03277560846110.589114337098-0.02094104620130.86970642037133.5501474797-2.174796682688.137119732
84.260758445574.322633164391.370175986645.18368311107-1.008165398712.0031771062-0.320179006865-0.5927474291570.671408449062-1.495883728390.3527896125890.36394272174.87057573755-2.80566147195-0.6591610649570.320169118701-1.14383059377-0.2080117238942.43437805082-0.4311938725552.258328526818.1113356741-7.316689064029.94976360065
92.158750702928.17008297042.048275953978.72146995158-2.483919330917.125067702430.616074767714-0.2180521536590.9632754843360.212475339054-0.6617759995892.56037813238-1.17443775285-1.113361261030.003297919637640.5680831605670.1423502483150.1269526096080.771348124885-0.07394997465941.2715707348129.93851207358.5801197083617.1194314169
108.622899539193.546994725314.004336264214.552242937561.941513223595.32454532184-0.7557707958580.270527183589-1.685145244150.3754532308640.359315421594-0.1707614946120.540489805385-1.14240399990.3080356968170.922246296533-0.3676177940370.119222650880.994171164180.08756817502051.1686978006822.4595168307-4.9078925309315.6857960743
116.885047047055.5234200245-1.58855266482.28883217941-3.741166676088.998459516570.821497505956-0.1679384690680.7086009884751.84374462669-0.9217233002780.46496778683-1.411495167540.0524719291818-0.03852633571260.6571752072510.09610527744610.02378765235240.337014142078-0.1129899839680.62794838214242.139468723227.79866204919.16716175786
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 9 )AA3 - 91 - 7
22chain 'A' and (resid 10 through 30 )AA10 - 308 - 28
33chain 'A' and (resid 31 through 60 )AA31 - 6029 - 58
44chain 'A' and (resid 61 through 70 )AA61 - 7059 - 66
55chain 'A' and (resid 71 through 89 )AA71 - 8967 - 85
66chain 'A' and (resid 90 through 108 )AA90 - 10886 - 104
77chain 'B' and (resid 1 through 32 )BD1 - 321 - 32
88chain 'B' and (resid 33 through 40 )BD33 - 4033 - 40
99chain 'B' and (resid 41 through 54 )BD41 - 5441 - 54
1010chain 'B' and (resid 55 through 94 )BD55 - 9455 - 85
1111chain 'B' and (resid 95 through 109 )BD95 - 10986 - 100

+
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