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- PDB-9cen: Structure of the thiocysteine lyase (SH) domain from guangnanmyci... -

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Basic information

Entry
Database: PDB / ID: 9cen
TitleStructure of the thiocysteine lyase (SH) domain from guangnanmycin A biosynthetic pathway
ComponentsPolyketide Synthase Protein
KeywordsBIOSYNTHETIC PROTEIN / thiocysteine lyase / polyketide synthase / natural product / sulfur incorporation.
Function / homology
Function and homology information


3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / DIM/DIP cell wall layer assembly / amino acid metabolic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / lyase activity / plasma membrane / cytoplasm
Similarity search - Function
Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / CurL-like, PKS C-terminal / Methyltransferase type 12 / Methyltransferase domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / : ...Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / CurL-like, PKS C-terminal / Methyltransferase type 12 / Methyltransferase domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / : / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / alpha/beta hydrolase fold / ClpP/crotonase-like domain superfamily / Alpha/beta hydrolase fold-1 / Acyl-CoA N-acyltransferase / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ACETATE ION / : / Uncharacterized protein
Similarity search - Component
Biological speciesStreptomyces sp. CB01883 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, G. / Chang, C. / Shen, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134954 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain.
Authors: Steele, A.D. / Meng, S. / Li, G. / Kalkreuter, E. / Chang, C. / Shen, B.
History
DepositionJun 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide Synthase Protein
B: Polyketide Synthase Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,57410
Polymers99,2212
Non-polymers3538
Water12,592699
1
B: Polyketide Synthase Protein
hetero molecules

A: Polyketide Synthase Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,57410
Polymers99,2212
Non-polymers3538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2820 Å2
ΔGint-16 kcal/mol
Surface area34860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.963, 89.555, 70.012
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyketide Synthase Protein


Mass: 49610.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CB01883 (bacteria) / Gene: AMK32_09510 / Variant: AA: 6689-7124 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1Q5KRT3
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.59 % / Description: Needles and clustered needles
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium Acetate, 0.1 M Tris:HCl, pH 8.5, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→40.77 Å / Num. obs: 73808 / % possible obs: 98.51 % / Redundancy: 3.26 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0438 / Rpim(I) all: 0.0313 / Rrim(I) all: 0.05784 / Net I/σ(I): 13.73
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.2309 / Num. unique obs: 7229 / CC1/2: 0.915 / CC star: 0.978 / Rpim(I) all: 0.1584 / Rrim(I) all: 0.2816 / % possible all: 96.59

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Processing

Software
NameVersionClassification
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YCN

2ycn


Resolution: 1.8→40.77 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 17.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.181 1732 2.35 %
Rwork0.147 --
obs0.148 73785 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 14 699 7077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.25121390.18215819X-RAY DIFFRACTION96
1.85-1.910.21041450.16326043X-RAY DIFFRACTION99
1.91-1.980.20821450.15555985X-RAY DIFFRACTION99
1.98-2.060.19121440.15135994X-RAY DIFFRACTION99
2.06-2.150.18061470.14185951X-RAY DIFFRACTION98
2.15-2.270.17821380.14116031X-RAY DIFFRACTION99
2.27-2.410.16831470.1426014X-RAY DIFFRACTION99
2.41-2.60.17881430.14875951X-RAY DIFFRACTION98
2.6-2.860.19811440.15556057X-RAY DIFFRACTION99
2.86-3.270.17491480.15086057X-RAY DIFFRACTION99
3.27-4.120.16731450.13156062X-RAY DIFFRACTION99
4.12-40.770.1681470.15016089X-RAY DIFFRACTION98
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)
12.34050.3427-0.46091.0034-0.08820.8402-0.12350.084-0.1141-0.14650.1119-0.08640.17310.1953-0.00920.18260.04260.00630.16590.01380.11353.35920.4407-37.2231
20.5582-0.0495-0.1481.29930.43811.90840.0309-0.03570.0227-0.0101-0.00410.0682-0.10920.002-0.02290.12140.01380.01850.1523-0.00140.1526-13.638515.0007-20.941
31.5170.37210.42150.36080.3391.2297-0.0781-0.17-0.15410.00240.052-0.0050.16810.03940.01540.1850.04270.0070.15080.01450.1203-7.9996-1.8862-27.1479
41.70770.146-0.45840.9974-0.72841.34180.075-0.50280.07630.1338-0.0946-0.1761-0.08660.4625-0.00540.13430.0344-0.01490.3608-0.02960.151912.98537.2081-22.4961
51.92641.3287-0.52792.4561-0.9961.3188-0.0339-0.41440.0403-0.0553-0.1521-0.27560.03490.54010.17560.20280.0661-0.00580.39830.01040.240420.32956.3861-28.7301
62.0918-0.0179-0.35270.60910.09320.6976-0.0921-0.1752-0.23910.07850.08630.080.083-0.06020.00780.13940.00610.01190.10580.01860.1169-24.77231.6807-49.7867
70.5887-0.0751-0.00311.6888-0.38430.59920.0087-0.00110.01060.0343-0.0121-0.0256-0.02480.02580.0010.0969-0.01440.00780.09220.0040.1069-9.061522.7616-58.7189
81.8243-0.4470.44790.5889-0.27121.2243-0.03960.1283-0.14610.00290.0317-0.0389-0.020.07850.01870.0927-0.00150.00180.03630.00310.0739-13.82064.8068-60.1969
90.5188-0.1157-0.05691.0531-0.16850.93090.10080.11410.22230.08430.02750.2742-0.3515-0.2657-0.09350.18210.04540.02350.18190.03240.223-35.582516.784-61.2313
101.3181-0.1088-0.030.6951-0.02740.8498-0.04350.00140.11170.08180.08470.2458-0.0807-0.238-0.0180.13740.03140.01850.17520.02960.2138-38.82310.3973-56.7113
117.32047.3061.73117.37151.29482.75590.75341.95651.26550.1388-0.57660.1399-0.15250.2366-0.17570.67350.0875-0.1510.7036-0.03340.6971-56.146220.1812-41.66
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 27 THROUGH 80 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 81 THROUGH 283 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 284 THROUGH 325 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 326 THROUGH 402 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 403 THROUGH 449 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 24 THROUGH 80 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 81 THROUGH 283 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 284 THROUGH 325 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 326 THROUGH 387 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 388 THROUGH 450 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 451 THROUGH 451 )

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