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- PDB-8h4q: Aspergillomarasmine A biosynthese complex with OPS -

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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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-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: Adv.Synth.Catal. / Year: 2024
Title: Investigation of AMA Synthase from Pyrenophora teres f. teres 0-1 for the Synthesis of Aspergillomarasmine A Analogues and Non-Canonical Amino Acids
Authors: Zhu, Z. / Ma, Y. / Xie, X. / Wang, Z. / Han, L. / Song, J. / Liang, Y. / Poelarends, G.J. / Chen, Y. / Lu, M. / Zhang, J.
History
DepositionOct 11, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationN

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Experimental details

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Experiment

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

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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

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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

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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

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