[English] 日本語
Yorodumi
- PDB-9moj: Saccharolobus solfataricus GINS tetramer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9moj
TitleSaccharolobus solfataricus GINS tetramer
Components
  • GINS subunit domain-containing protein
  • SsoGINS51
KeywordsREPLICATION / GINS / DNA replication
Function / homologyGINS complex, subunit Psf3 superfamily / GINS subunit, domain A / GINS complex protein helical bundle domain / GINS subunit domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesSaccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEnemark, E.J. / Shankar, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136313 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM152281 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structure of the Saccharolobus solfataricus GINS tetramer.
Authors: Shankar, S. / Enemark, E.J.
History
DepositionDec 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SsoGINS51
B: SsoGINS51
C: GINS subunit domain-containing protein
D: GINS subunit domain-containing protein


Theoretical massNumber of molelcules
Total (without water)76,9704
Polymers76,9704
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-116 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.236, 180.236, 51.203
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

#1: Protein SsoGINS51


Mass: 17836.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Gene: SSO1049 / Plasmid: pEE093
Details (production host): pET-duet construct of GINS51/GINS23 both untagged
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -RIPL / References: UniProt: Q97Z82
#2: Protein GINS subunit domain-containing protein


Mass: 20648.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Gene: Ssol_1833 / Plasmid: pEE093
Details (production host): pET-duet construct of GINS51/GINS23 both untagged
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -RIPL / References: UniProt: D0KTH8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.18 M tri-Ammonium citrate 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42463 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 37.3 % / Biso Wilson estimate: 52.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.085 / Net I/σ(I): 34.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 19 % / Rmerge(I) obs: 1.091 / Mean I/σ(I) obs: 1 / Num. unique obs: 1957 / CC1/2: 0.817 / Rrim(I) all: 1.116 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→31.22 Å / SU ML: 0.299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2428 1904 4.88 %
Rwork0.2199 37080 -
obs0.2211 38984 91.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 0 5 5309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00165370
X-RAY DIFFRACTIONf_angle_d0.38597216
X-RAY DIFFRACTIONf_chiral_restr0.0386856
X-RAY DIFFRACTIONf_plane_restr0.0026892
X-RAY DIFFRACTIONf_dihedral_angle_d11.21042118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.37161120.30432256X-RAY DIFFRACTION78.1
2.36-2.420.30121200.27752389X-RAY DIFFRACTION82.72
2.42-2.490.26111100.27782496X-RAY DIFFRACTION86.06
2.49-2.570.29591460.26562530X-RAY DIFFRACTION87.82
2.57-2.660.30511280.27722599X-RAY DIFFRACTION90.57
2.66-2.770.30071330.2712656X-RAY DIFFRACTION92.14
2.77-2.90.28261160.27252698X-RAY DIFFRACTION92.54
2.9-3.050.28751620.26812692X-RAY DIFFRACTION93.51
3.05-3.240.31731230.28212796X-RAY DIFFRACTION95.64
3.24-3.490.28951350.25812799X-RAY DIFFRACTION96.58
3.49-3.840.25841440.22612819X-RAY DIFFRACTION96.58
3.84-4.390.2251660.22848X-RAY DIFFRACTION97.73
4.39-5.530.20931560.18552805X-RAY DIFFRACTION96.01
5.53-31.220.18181530.16272697X-RAY DIFFRACTION89.09
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)
11.055495545880.705553330107-0.003902161002061.326486429960.0469868206686-0.037974977004-0.546463532056-0.1937618973280.4537491189160.4735983998730.388236209270.362537132763-1.00204990003-0.6659222579560.0003989841198150.7417878159640.107119061847-0.1641119794450.6347109679480.02527602400280.728992955789-12.4228939414-51.75133147810.909597429076
20.639169799298-0.720201796206-0.4976582848270.8802356209490.3155789984580.594257513054-0.1305892604960.5025524486410.414691309411-0.132854439138-0.0731270529558-0.2873679766270.3315020544810.162892175938-0.01901256348150.502473778124-0.0820788804236-0.1606961290170.6563894319970.14393813660.555672936109-5.53161978254-57.148524448-5.39625450305
30.031013044882-0.01317960820680.3642209964950.0325388426753-0.09846301448240.800770831791-0.389179096021-0.07416022150840.04363595604180.9387578394850.4535368215480.1898919276460.0870428067937-0.279293338106-0.02409614049170.4198887397980.135165173688-0.0263515826670.3695244410040.02718562852370.483155532022-6.75075624726-72.69535064158.75726770997
41.53483994237-0.315979950572-0.2939069162822.3345410371-1.179590746121.60336072205-0.2150034083690.3044189637380.0649561686757-0.2263474935530.3196970986750.9050598345810.353425535117-0.160510306915-0.005270508369430.404972549895-0.0535759519144-0.1024798665280.4686049092240.03724396034580.606684011121-13.3214044332-90.17326058654.02284124168
50.5291869165020.1835572143470.01316020220930.4984357338120.5666722845940.562857377725-0.06815615784180.903864702719-0.386019728835-0.94596073444-0.120722978412-0.8576418743620.2323440382720.671491179705-4.08987182437E-50.571761221871-0.0113237234018-0.05151788481520.5403453708240.04325056106880.61231556186512.4538480049-80.28749853251.55950315998
60.2154679822110.2660901092740.3913464717610.673440179940.4343110203710.5718622612910.2278751242960.0672024790615-0.0635530353806-0.208619708059-0.685849402813-0.184231269330.1068372389651.05370160417-0.00176828060080.517789007127-0.04009404978860.05627091144220.4915930112790.06155568573160.6548413477476.01356108376-95.25521022689.62105592296
70.909804786595-0.1335536583840.1633125094020.4382542076440.1672686819080.567626365099-0.289251582248-0.2885405083180.1366287159930.6144923735120.0111844272461-0.143313659344-0.201780128434-0.350228447971.78719371631E-50.484843777702-0.0231931389617-0.06483143500430.436148321071-0.02799524357330.3306884738826.06350530315-80.570166813812.155437518
8-0.01002001999370.0207988610427-0.07531982750860.0228944308591-0.1231106585030.3959597260490.2107794067460.2589466913570.512136338189-0.651733891133-0.0919189512479-0.05154501177180.00772892548186-0.211030023586-0.0001731190698520.4047991277190.0143503275724-0.106994278490.397117647568-0.002091063033380.565690545558-4.77689425581-72.0456553793-4.02606378462
91.068989034940.352132837691-0.8439781561170.581595391368-0.5198207760510.720954292740.02961625026790.2083329987390.0677294808225-0.312447528370.33144856981.586998149130.108137022533-0.5160803304610.4259813349270.4727734536-0.0511216367207-0.2557715391670.6680018396040.2074153185851.10361848045-24.5800342352-71.7499381476-3.17579723346
100.09552176009910.5073817284040.3234489514012.894291445851.871869801631.209085437860.4298053812750.529584488391-0.301383992593-1.38777425963-0.199388734785-0.483220071079-0.5328619721620.7088995474580.7932175947370.8719525244020.102014250946-0.2211361485030.8943923570680.3019519268440.990915720275-20.6349710371-61.0132374401-15.1816471227
113.016271816070.2523641411290.6503740229360.724714402024-0.5281819935290.686093212318-0.236643107096-1.060209401011.05021745770.885123168595-0.2017452647210.475190263442-0.927118817989-0.533343468898-0.01477946981120.56628077799-0.0708903183861-0.195890772420.4243982703540.009222821556940.49912981947712.1487200767-72.775825425812.868852583
120.6018617715381.131093630060.5330119297512.987890120260.6006313067961.931837752860.3200431254950.0978427908519-0.549605328810.932694713605-0.405193176251-2.196451020160.06379338954240.583310426495-0.1044525108880.766845277525-0.110878770989-0.3593937657810.5939352179980.104046218240.85736075690921.9482720366-93.085134747322.3242885725
130.446880502696-0.130969146445-0.3365524658141.028176999160.2328823509111.272326817790.253964125179-0.789645812971-0.174392194567-0.08697611630050.339752553427-0.9152374792251.084979329640.361488840533.338757460890.934186595387-0.30189084711-0.8384471671260.6278222963360.06543591764620.97874667438833.5711889166-76.043450608423.5010827974
140.303972196904-0.3237659173620.129148638080.266148721098-0.1788126726080.139135654559-0.09928797974140.0146508653326-0.475617959353-0.1390540479580.219434096744-0.7150224897970.4579788638820.4964726275130.0002749972881790.81151371803-0.17416368759-0.1109581359070.717550562081-0.1388096906551.1154253371934.6008282077-67.635777190610.4739395529
151.07214586042-0.9176436156720.277778730210.765089921843-0.2555488530020.08687523056710.0639628178319-1.811955105640.0696797345251.13036280529-0.3520758179150.8159396108310.811635562816-0.638826129244-0.07786161708641.1584477522-0.422577530309-0.09546888151071.14033554371-0.01735938927690.55925234109824.2073689248-73.768832013229.4607825275
161.56246659152-0.480630969506-0.7848789092650.323973292540.1899712111121.974346646860.0170561630356-0.4700280232240.6183109215230.611962506154-0.114286795025-0.84251199781-0.524078361537-0.2194625768570.8893278544740.824075059384-0.205024921817-0.2904401370110.734958045955-0.150011789680.69037232546330.4759299473-63.096389238120.1616209001
170.460845623663-0.323928075553-1.144668369340.4922315055370.9979884340963.38888294976-0.0675433177525-0.152290148355-0.5192883439930.494910094356-0.279697009594-0.3145140748591.033251404230.346023641138-0.0261350267490.617027100012-0.165853651777-0.1570101118780.67688813286-0.1495815981020.90949486542430.1102219865-71.07793057732.1871352377
180.2170439318410.4085978827920.2257975165950.6047844636880.3214265279670.1501067761160.436842392945-0.0147017594125-0.485644959849-0.7115034233090.1401118678810.6662084788910.7117592270890.0208261591208-0.0001889497388380.576257221549-0.1337728736-0.1310675882530.611190512855-0.1370422904080.71243094855619.2285774995-62.06290808460.538462348006
191.476812160331.55984096043-0.3111070938471.67863274656-0.3068152679190.0822662512177-0.159746778170.908807176456-1.31962869123-0.309883017666-0.0306472683706-1.184946570660.2422286827620.68571007265-0.09249392735460.585205511328-0.165693386944-0.1591329698110.6830758183840.08342308781560.7793038043464.36271995365-55.1460081848-3.43232468386
203.301367377031.856995508260.8245574120531.84378367122-0.4653070475711.75174863770.02256012883440.4443259367872.128454118230.277268810898-0.1480123410660.919102916322-1.02066169362-0.0589099361704-0.241492096870.994766767545-0.100448486429-0.4702930170630.9852543875690.5791345553561.12200294704-4.36518944945-36.9123483102-15.2142241824
210.2941740115710.05173852936060.1614119953940.0903316066641-0.0290494724690.516872270774-0.2337418306670.8597243681121.51505698836-0.3148621154070.229164640259-0.0851825770872-0.8814653359770.1936259603140.03013221241660.669786324156-0.246063181835-0.1058748794290.7855958432060.0550029388160.84034208420322.8286694061-40.4176883055-3.92024240528
220.2808184044330.7170123312210.5070258653992.091693572431.06381539871.97235965681-0.3029282287670.7439157652030.106103520477-1.116572237390.42928168025-0.32320211881.026725878940.619086493096-0.1426073596161.03182524862-0.371826460341-0.1634266624030.9822903538330.1145648852920.52416124646318.4044461321-48.1577688723-11.6038380885
231.23960718553-0.4520836823040.3582733927541.397449771-1.854329440472.57871691549-0.414066934678-1.39595547651.384363656681.687244448841.492138728920.23429420709-1.7693867803-1.077705046660.274079764941.024006511810.0546903009487-0.09873189704030.834842354025-0.1509205956440.96320020466415.8168649307-43.55575500329.73414478394
240.226757169240.215951609337-0.07686369810380.556357938-0.1185692220560.4805365898110.100301194506-0.2514197195810.1747983542250.4365953817920.4876420919710.96340238141-0.211784429428-0.3434691955260.0300760371350.616826527777-0.131862626775-0.1227527857170.7309128327970.07293091378120.56760957608415.3246911126-56.560278724410.6264527329
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 38 )AAAAA1 - 381 - 38
22chain 'A' and (resid 39 through 66 )AAAAA39 - 6639 - 66
33chain 'A' and (resid 67 through 92 )AAAAA67 - 9267 - 92
44chain 'A' and (resid 93 through 148 )AAAAA93 - 14893 - 148
55chain 'B' and (resid 1 through 19 )BBBBB1 - 191 - 19
66chain 'B' and (resid 20 through 38 )BBBBB20 - 3820 - 38
77chain 'B' and (resid 39 through 66 )BBBBB39 - 6639 - 66
88chain 'B' and (resid 67 through 92 )BBBBB67 - 9267 - 92
99chain 'B' and (resid 93 through 142 )BBBBB93 - 14293 - 142
1010chain 'B' and (resid 143 through 148 )BBBBB143 - 148143 - 148
1111chain 'C' and (resid 1 through 15 )CCCCC1 - 151 - 15
1212chain 'C' and (resid 16 through 56 )CCCCC16 - 5616 - 56
1313chain 'C' and (resid 57 through 80 )CCCCC57 - 8057 - 80
1414chain 'C' and (resid 81 through 94 )CCCCC81 - 9481 - 94
1515chain 'C' and (resid 95 through 111 )CCCCC95 - 11195 - 111
1616chain 'C' and (resid 112 through 142 )CCCCC112 - 142112 - 142
1717chain 'C' and (resid 143 through 154 )CCCCC143 - 154143 - 154
1818chain 'C' and (resid 155 through 176 )CCCCC155 - 176155 - 176
1919chain 'D' and (resid 1 through 15 )DDDDD1 - 151 - 15
2020chain 'D' and (resid 16 through 67 )DDDDD16 - 6716 - 67
2121chain 'D' and (resid 68 through 94 )DDDDD68 - 9468 - 94
2222chain 'D' and (resid 95 through 142 )DDDDD95 - 14295 - 142
2323chain 'D' and (resid 143 through 154 )DDDDD143 - 154143 - 154
2424chain 'D' and (resid 155 through 174 )DDDDD155 - 174155 - 174

+
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