[English] 日本語
Yorodumi
- PDB-9nev: Acanthamoeba Polyphaga Mimivirus L230 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nev
TitleAcanthamoeba Polyphaga Mimivirus L230
ComponentsProcollagen lysyl hydroxylase and glycosyltransferase
KeywordsVIRAL PROTEIN / L230
Function / homology
Function and homology information


procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase activity / L-ascorbic acid binding / Transferases; Glycosyltransferases; Hexosyltransferases / iron ion binding
Similarity search - Function
Glycosyl transferase, family 25 / Glycosyltransferase family 25 (LPS biosynthesis protein) / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Procollagen lysyl hydroxylase and glycosyltransferase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, T. / Buhlheller, C. / Guo, H.
Funding support United States, 3items
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
American Cancer SocietyRSG-24-1156098-01-MM United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structure of an Fe 2+ -binding-deficient mimiviral collagen lysyl hydroxylase.
Authors: Chen, T. / Buhlheller, C. / Guo, H.
History
DepositionFeb 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Procollagen lysyl hydroxylase and glycosyltransferase
B: Procollagen lysyl hydroxylase and glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)54,5582
Polymers54,5582
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-8 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.610, 109.610, 84.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 682 - 895 / Label seq-ID: 22 - 235

Dom-ID
1
2

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

-
Components

#1: Protein Procollagen lysyl hydroxylase and glycosyltransferase / LHGT / Lysyl hydroxylase / Procollagen-lysine / 2-oxoglutarate 5-dioxygenase


Mass: 27278.756 Da / Num. of mol.: 2 / Mutation: H825A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_L230 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5UQC3, procollagen-lysine 5-dioxygenase, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein/cofactor mix: 15mg/ml L230, 500uM FeCl2 Mother Liquor: 0.04 M potassium dihydrogen phosphate, 16 % w/v PEG 8000, 20 % v/v Glycerol The ratio of mix and mother liquor was at 1:1.

-
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: Apr 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.02 Å / Num. obs: 23603 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Net I/σ(I): 15.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 27.1 % / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2273 / CC1/2: 0.936 / % possible all: 100

-
Processing

Software
NameVersionClassification
DIALS3.8.0data collection
xia23.8.0data reduction
Aimless0.7.8data scaling
PHENIX1.20.1phasing
PHASER2.8.3phasing
Coot0.9.8.93model building
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.015 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.609 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.231 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2509 1210 5.139 %
Rwork0.2047 22336 -
all0.207 --
obs-23546 99.877 %
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: 33.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.116 Å20 Å20 Å2
2---0.116 Å20 Å2
3---0.232 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 0 145 3443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123416
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.844641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3545397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.809512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85210568
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.62310174
X-RAY DIFFRACTIONr_chiral_restr0.1120.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022664
X-RAY DIFFRACTIONr_nbd_refined0.1870.21275
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2132
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.28
X-RAY DIFFRACTIONr_mcbond_it2.7483.1031582
X-RAY DIFFRACTIONr_mcangle_it4.2175.5611972
X-RAY DIFFRACTIONr_scbond_it4.0643.4551834
X-RAY DIFFRACTIONr_scangle_it6.1946.1292666
X-RAY DIFFRACTIONr_lrange_it7.70731.7934967
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.056460
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.09540.05009
12AX-RAY DIFFRACTIONLocal ncs0.09540.05009
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
2.3-2.360.373810.26416160.26917000.9060.95799.82350.228
2.36-2.4240.316940.23615860.2416810.9430.96599.94050.206
2.424-2.4940.384690.23915330.24516040.9190.96499.87530.207
2.494-2.5710.293780.25114970.25315770.9470.96499.87320.214
2.571-2.6550.271780.23814410.2415210.9620.96699.86850.203
2.655-2.7480.266730.2214010.22214740.9580.9711000.19
2.748-2.8510.238860.21513540.21714400.9590.9721000.189
2.851-2.9670.262820.21812900.22113720.950.9711000.189
2.967-3.0990.231760.20212490.20413260.9630.97499.92460.181
3.099-3.2490.242490.21712280.21812780.9580.97199.92180.199
3.249-3.4240.258640.22111530.22312170.9650.9731000.209
3.424-3.6310.243730.20110680.20411410.9660.9781000.193
3.631-3.880.252550.20610470.20911030.9570.97899.90930.2
3.88-4.1880.292400.1839780.18710180.9520.9821000.179
4.188-4.5850.177460.1528930.1539390.9840.9871000.15
4.585-5.120.198390.1368250.1398640.9780.9891000.138
5.12-5.9020.226470.1837220.1857700.9710.98399.87010.183
5.902-7.2020.234270.2356390.2356670.9660.97399.85010.231
7.202-10.0770.211370.2024930.2035300.9780.981000.21
10.077-49.0150.292160.2323220.2343380.8980.9541000.257

+
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