[English] 日本語
Yorodumi
- PDB-8h4h: The apo structure of Aspergillomarasmine A synthetase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h4h
TitleThe apo structure of Aspergillomarasmine A synthetase
ComponentsRhodanese domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / synthase / PLP-dependent enzyme
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
PYRIDOXAL-5'-PHOSPHATE / Rhodanese domain-containing protein
Similarity search - Component
Biological speciesPyrenophora teres f. teres 0-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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: The apo structure of Aspergillomarasmine A synthetase at 2.3 Angstroms resolution
Authors: Lu, M. / Zhang, J. / Wang, Z. / Han, L.
History
DepositionOct 10, 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)117,8344
Polymers117,3392
Non-polymers4942
Water50428
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)235,6678
Polymers234,6794
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)71.890, 264.099, 163.368
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: 58669.703 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate, 1.8 M 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 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→81.68 Å / Num. obs: 132471 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 52 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.36 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5035 / CC1/2: 0.862

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDS2.3.0.20200229data reduction
Aimless0.7.4data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→81.68 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 3305 2.49 %
Rwork0.2399 129166 -
obs0.2405 132471 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.9 Å2 / Biso mean: 77.6889 Å2 / Biso min: 45.62 Å2
Refinement stepCycle: final / Resolution: 2.3→81.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7408 0 30 28 7466
Biso mean--78.78 81.61 -
Num. residues----959
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.330.52071410.45775364550599
2.33-2.370.46961400.44075392553299
2.37-2.40.46411350.404454165551100
2.4-2.440.39461390.38865393553299
2.44-2.490.4011350.377454285563100
2.49-2.530.38591340.358653555489100
2.53-2.580.39581350.36395411554699
2.58-2.630.40681410.343354095550100
2.63-2.690.31181380.32855362550099
2.69-2.750.33711380.31345371550999
2.75-2.820.36471330.3155391552499
2.82-2.90.40081410.307254095550100
2.9-2.980.39831380.290754215559100
2.98-3.080.34011340.283553655499100
3.08-3.190.2871420.28775421556399
3.19-3.320.28441360.26265350548699
3.32-3.470.22781410.244154195560100
3.47-3.650.30591390.24553955534100
3.65-3.880.21621360.23135415555199
3.88-4.180.21351370.19745314545198
4.18-4.60.16851420.18045391553399
4.6-5.270.21181350.18215390552599
5.27-6.630.22421390.20355372551199
6.63-81.680.1941360.16945212534896
Refinement TLS params.Method: refined / Origin x: 1.8259 Å / Origin y: -34.7161 Å / Origin z: -40.5349 Å
111213212223313233
T0.507 Å2-0.0085 Å2-0.0152 Å2-0.5767 Å20.0023 Å2--0.5282 Å2
L0.069 °20.0277 °20.0484 °2-0.8071 °20.0629 °2--0.0133 °2
S-0.0257 Å °-0.0131 Å °0.0612 Å °-0.0507 Å °0.0109 Å °-0.0089 Å °-0.0445 Å °-0.0173 Å °0.016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allN2 - 487
2X-RAY DIFFRACTION1allA4 - 486
3X-RAY DIFFRACTION1allB2 - 3
4X-RAY DIFFRACTION1allS1 - 48

+
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