[English] 日本語
Yorodumi
- PDB-8wpo: Anabaena McyI R166A with prebound NAD and citrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wpo
TitleAnabaena McyI R166A with prebound NAD and citrate
ComponentsMcyI
KeywordsOXIDOREDUCTASE / hepatotoxin / microcystin / cofactor / Anabaena
Function / homologyCITRATE ANION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesAnabaena sp. 90 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, X. / Yin, Y. / Duan, Y. / Liu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI.
Authors: Wang, X. / Yin, Y. / Cheng, W.L. / Duan, Y.F. / Li, Y.S. / Wang, J. / Wang, M. / Dai, H.E. / Liu, L.
History
DepositionOct 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4724
Polymers38,8761
Non-polymers1,5963
Water5,170287
1
A: McyI
hetero molecules

A: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9448
Polymers77,7522
Non-polymers3,1926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10160 Å2
ΔGint-35 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.506, 61.506, 173.007
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-595-

HOH

-
Components

#1: Protein McyI


Mass: 38875.832 Da / Num. of mol.: 1 / Mutation: R166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. 90 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M tAmSO4, 0.1 M tri-Sodium citrate , pH 5.6, 15% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23011 / % possible obs: 99.6 % / Redundancy: 19.1 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.021 / Rrim(I) all: 0.092 / Χ2: 0.98 / Net I/σ(I): 6 / Num. measured all: 440407
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.1819.81.57322430.7310.9190.3561.6130.81199.2
2.18-2.2618.71.23622570.9110.9760.2931.2711.2999.3
2.26-2.3719.20.89522800.9270.9810.2070.9190.87599.4
2.37-2.4920.20.49222120.9710.9930.110.5040.8699.5
2.49-2.6519.60.32522690.9850.9960.0740.3330.91299.6
2.65-2.8518.60.21722840.9910.9980.0510.2230.95299.6
2.85-3.1419.80.13623020.9970.9990.0310.1391.03599.8
3.14-3.59190.09223100.9970.9990.0210.0941.11999.8
3.59-4.5219.30.07123510.9980.9990.0160.0731.149100
4.52-5017.40.05225030.99910.0130.0530.80199.7

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WWK

1wwk


Resolution: 2.1→39.13 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1225 5.46 %
Rwork0.2256 --
obs0.2272 22448 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 105 287 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042581
X-RAY DIFFRACTIONf_angle_d0.7683534
X-RAY DIFFRACTIONf_dihedral_angle_d16.736934
X-RAY DIFFRACTIONf_chiral_restr0.046424
X-RAY DIFFRACTIONf_plane_restr0.005442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.32141440.30322057X-RAY DIFFRACTION88
2.18-2.280.39721250.42382209X-RAY DIFFRACTION93
2.28-2.40.32521250.27442348X-RAY DIFFRACTION100
2.4-2.550.31431400.26292385X-RAY DIFFRACTION100
2.55-2.750.26871400.25592363X-RAY DIFFRACTION100
2.75-3.030.27161590.24172381X-RAY DIFFRACTION100
3.03-3.470.27751590.21132400X-RAY DIFFRACTION100
3.47-4.370.21311010.17432487X-RAY DIFFRACTION100
4.37-39.130.16881320.16992593X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.5181 Å / Origin y: 8.1137 Å / Origin z: -4.63 Å
111213212223313233
T0.1659 Å20.0912 Å20.1624 Å2-0.0321 Å2-0.1236 Å2--0.1125 Å2
L0.1544 °2-0.0513 °2-0.0175 °2-0.155 °2-0.0528 °2--0.0443 °2
S0.1604 Å °-0.174 Å °0.12 Å °-0.2251 Å °0.0318 Å °0.0869 Å °-0.2329 Å °-0.0187 Å °0.1571 Å °
Refinement TLS groupSelection details: all

+
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