[English] 日本語
Yorodumi
- PDB-8h4q: Aspergillomarasmine A biosynthese complex with OPS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h4q
TitleAspergillomarasmine A biosynthese complex with OPS
ComponentsRhodanese domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Aspergillomarasmine A biosynthese
Function / homology
Function and homology information


Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
Chem-P1T / Rhodanese domain-containing protein
Similarity search - Component
Biological speciesPyrenophora teres f. teres 0-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsLu, M. / Zhang, J. / Wang, Z. / Han, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82003627 China
National Science Foundation (NSF, China)BK20200565 China
CitationJournal: To Be Published
Title: Aspergillomarasmine A biosynthese complex with OPS
Authors: Lu, M. / Zhang, J. / Wang, Z. / Han, L.
History
DepositionOct 11, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
N: Rhodanese domain-containing protein
A: Rhodanese domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3184
Polymers115,6822
Non-polymers6362
Water19811
1
N: Rhodanese domain-containing protein
A: Rhodanese domain-containing protein
hetero molecules

N: Rhodanese domain-containing protein
A: Rhodanese domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,6368
Polymers231,3634
Non-polymers1,2734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area19720 Å2
ΔGint-89 kcal/mol
Surface area69120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.125, 264.071, 163.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Rhodanese domain-containing protein


Mass: 57840.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrenophora teres f. teres 0-1 (fungus)
Gene: PTT_12124 / Production host: Escherichia coli (E. coli) / References: UniProt: E3RT21
#2: Chemical ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium acetate, 1.8M sodium formate / PH range: 5.0-5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→102.82 Å / Num. obs: 147718 / % possible obs: 99.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 54.65 Å2 / CC1/2: 1 / Net I/σ(I): 22.4
Reflection shellResolution: 2.2→2.32 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5281 / CC1/2: 0.85

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: SAD / Resolution: 2.22→24.19 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 3805 2.58 %
Rwork0.2155 143911 -
obs0.216 147716 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.96 Å2 / Biso min: 45.92 Å2
Refinement stepCycle: final / Resolution: 2.22→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7486 0 42 11 7539
Biso mean--66.25 67.23 -
Num. residues----969
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.22-2.240.4804129499593
2.24-2.270.46151360.44685323100
2.27-2.30.46121430.44155349100
2.3-2.340.42141410.41855345100
2.34-2.370.44161410.41115366100
2.37-2.410.40421400.3925332100
2.41-2.450.33861455351100
2.45-2.490.34961380.34415334100
2.49-2.540.32881425362100
2.54-2.580.3681370.33885324100
2.58-2.640.35571450.32545372100
2.64-2.690.33281430.30645288100
2.69-2.760.30741390.29075349100
2.76-2.830.34851420.29355321100
2.83-2.90.30091440.27485314100
2.9-2.990.36541430.26315413100
2.99-3.080.28461430.26965311100
3.08-3.190.33481410.24875356100
3.19-3.320.21971405339100
3.32-3.470.26251430.22295310100
3.47-3.650.20541425342100
3.65-3.880.25031410.18785406100
3.88-4.180.18471430.17365344100
4.18-4.60.15091345327100
4.6-5.260.17991430.15655358100
5.26-6.60.18461400.17115336100
6.6-24.190.15231470.14215344100
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)
10.6231-0.19570.06281.49230.05634.1070.0685-0.1255-0.07770.3050.06660.10770.0114-0.2976-0.12380.5398-0.0172-0.02970.64120.03480.595-3.808-79.07-26.847
21.82520.5558-1.01561.6232-0.92951.69020.3346-0.17880.06870.1612-0.1897-0.0681-0.41680.1171-0.13870.9125-0.05850.17680.7299-0.05480.69314.838-46.929-72.361
32.14680.4872-0.43070.2349-0.08581.54130.0116-0.01070.0569-0.03060.05180.0226-0.50910.0776-0.02950.8462-0.0466-0.0590.61670.00640.89365.35419.1-44.369
41.5010.2718-0.6682.03860.44641.37380.00490.4650.0506-0.4508-0.00830.09570.014-0.1225-0.00450.73930.034-0.09180.7770.00710.7516-4.2222.981-62.041
51.2232-0.2731-0.43410.866-0.50131.10260.12730.19050.1782-0.31-0.0801-0.1715-0.20770.1179-0.06970.8928-0.0695-0.01470.66050.03340.872113.53614.687-58.158
60.23610.30430.31710.70660.63710.7485-0.0430.0107-0.0523-0.30360.0589-0.1417-0.2970.22950.0120.7093-0.0646-0.01480.76510.03740.834221.36510.369-48.922
70.70940.8583-0.60770.9117-0.7191.30170.0391-0.1060.1238-0.07830.02860.12330.14030.0091-0.07220.7225-0.0058-0.0520.64110.03280.78373.13-5.193-30.874
81.1186-0.0527-0.64822.0647-1.10612.6364-0.08480.0172-0.1508-0.0474-0.06660.27020.24520.03430.14430.8422-0.0165-0.01460.72680.01170.8337-12.029-24.233-10.563
91.21640.14050.15890.95760.30751.7251-0.0507-0.46510.17470.2536-0.06810.1306-0.43730.04670.09860.9918-0.0673-0.0130.9391-0.06550.9092-16.401-20.6290.007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN N AND RESID 1:340 )N1 - 340
2X-RAY DIFFRACTION2( CHAIN N AND RESID 341:488 )N341 - 488
3X-RAY DIFFRACTION3( CHAIN A AND RESID 3:59 )A3 - 59
4X-RAY DIFFRACTION4( CHAIN A AND RESID 60:168 )A60 - 168
5X-RAY DIFFRACTION5( CHAIN A AND RESID 169:244 )A169 - 244
6X-RAY DIFFRACTION6( CHAIN A AND RESID 245:308 )A245 - 308
7X-RAY DIFFRACTION7( CHAIN A AND RESID 309:360 )A309 - 360
8X-RAY DIFFRACTION8( CHAIN A AND RESID 361:461 )A361 - 461
9X-RAY DIFFRACTION9( CHAIN A AND RESID 462:491 )A462 - 491

+
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://pdbjlvh1.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