[English] 日本語
Yorodumi
- PDB-9crz: Acanthamoeba Polyphaga Mimivirus R655 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9crz
TitleAcanthamoeba Polyphaga Mimivirus R655
ComponentsPutative glycosyltransferase R655
KeywordsVIRAL PROTEIN / R655
Function / homologyGlycosyl transferase, family 25 / Glycosyltransferase family 25 (LPS biosynthesis protein) / Transferases / : / glycosyltransferase activity / : / URIDINE-5'-DIPHOSPHATE / Putative glycosyltransferase R655
Function and homology information
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMorin, K.H. / Buhlheller, C. / Kim, J.S. / Richards, S.J. / Guo, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R00CA225633 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R37CA278989 United States
CitationJournal: To Be Published
Title: Acanthamoeba Polyphaga Mimivirus R655
Authors: Kim, J.S. / Buhlheller, C. / Morin, K.H. / Gilliam, M.E. / Zhang, B. / Richards, S.J. / Miller, T.M. / Guo, H.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative glycosyltransferase R655
B: Putative glycosyltransferase R655
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6826
Polymers79,7642
Non-polymers9184
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.634, 96.213, 133.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 324 / Label seq-ID: 25 - 346

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Putative glycosyltransferase R655


Mass: 39882.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R655 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UQ62, Transferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: R655 IMAC elution fractions were digested with PreScission, and the His6 tag was removed by subtraction IMAC. Subtraction IMAC elution fractions were combined and concentrated for crystal ...Details: R655 IMAC elution fractions were digested with PreScission, and the His6 tag was removed by subtraction IMAC. Subtraction IMAC elution fractions were combined and concentrated for crystal trials. Single crystals were obtained through hanging drop vapor diffusion with the Mosquito liquid handling robot (TTPLabtech), utilizing a 200-nL drop with 1:1 mixture of protein solution and mother liquor at 277K. The protein solution has R655 (30 mg/mL) supplemented with 2 mM manganese(II) chloride and 2 mM UDP glucose. The mother liquor has 0.2 M magnesium formate, 20% (w/v) PEG 3350. To harvest the crystals, the crystals were soaked in a 1:1 mixture of 50% glycerol and mother liquor for 2 minutes and cooled in liquid nitrogen.

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→78.17 Å / Num. obs: 46085 / % possible obs: 99.6 % / Redundancy: 5.1 % / CC1/2: 0.946 / Net I/σ(I): 6.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3706 / CC1/2: 0.706 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
DIALS3.8.0data collection
xia23.8.0data reduction
Aimless0.7.8data scaling
PHENIX1.20.1phasing
PHASER2.8.3phasing
Coot0.9.8.92model building
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→78.167 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.896 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.194 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2518 2234 4.857 %
Rwork0.2096 43766 -
all0.212 --
obs-46000 99.198 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.652 Å2
Baniso -1Baniso -2Baniso -3
1-0.623 Å2-0 Å2-0 Å2
2---2.289 Å20 Å2
3---1.667 Å2
Refinement stepCycle: LAST / Resolution: 2.1→78.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 52 451 5617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125316
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.8217206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.085530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73910922
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.65110266
X-RAY DIFFRACTIONr_chiral_restr0.0880.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024026
X-RAY DIFFRACTIONr_nbd_refined0.1910.22428
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2487
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.220
X-RAY DIFFRACTIONr_mcbond_it1.5882.9972505
X-RAY DIFFRACTIONr_mcangle_it2.3885.3723126
X-RAY DIFFRACTIONr_scbond_it2.2813.1912811
X-RAY DIFFRACTIONr_scangle_it3.5395.7924080
X-RAY DIFFRACTIONr_lrange_it5.10537.5928430
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.0510553
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.087040.05009
12AX-RAY DIFFRACTIONLocal ncs0.087040.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.2731660.26431640.26433690.9370.94598.84240.252
2.154-2.2130.3091370.24531400.24732850.920.95399.75650.23
2.213-2.2780.3111540.25430420.25732120.9310.95299.50190.237
2.278-2.3480.3281640.2429490.24431270.9380.95999.55230.224
2.348-2.4250.2851400.24328900.24430340.9460.95999.86820.225
2.425-2.510.2731620.23227200.23528970.9520.96399.48220.215
2.51-2.6040.3061320.23926680.24228300.9410.96298.93990.222
2.604-2.710.2711340.21325860.21627220.9630.9799.92650.196
2.71-2.8310.2751320.21424880.21826290.9510.97199.65770.201
2.831-2.9690.2641060.20824030.2125110.9480.97199.92030.194
2.969-3.1290.3031120.2222580.22423710.9440.96899.95780.206
3.129-3.3180.2361300.21921460.2222880.9650.97299.47550.212
3.318-3.5470.1981040.20520390.20521580.9770.97899.30490.201
3.547-3.8310.245860.19618550.19819860.9640.97997.73410.195
3.831-4.1950.228880.17717540.1818540.9670.98199.35280.175
4.195-4.6890.194790.15615810.15816760.9760.98599.04530.156
4.689-5.4110.186630.16214160.16314960.9780.98198.86360.161
5.411-6.6190.275700.21311840.21612880.970.97697.36020.21
6.619-9.3270.265440.2149310.21610130.9760.97596.24880.217
9.327-78.1670.215310.2535530.2516180.9240.93394.49840.245

+
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