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- PDB-6l3m: Crystal Structure of the acyltransferase domain from the third mo... -

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Basic information

Entry
Database: PDB / ID: 6l3m
TitleCrystal Structure of the acyltransferase domain from the third module of the ansamitocin polyketide synthase
ComponentsPolyketide synthase
KeywordsTRANSFERASE / Polyketide / acyltransferase / ACP-linked extender unit / carrier specificity / biosynthesis
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #3290 / CurL-like, PKS C-terminal / SRCR domain profile. / SRCR domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : ...Alpha-Beta Plaits - #3290 / CurL-like, PKS C-terminal / SRCR domain profile. / SRCR domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-methoxypropanedioic acid / PHOSPHATE ION / Polyketide synthase
Similarity search - Component
Biological speciesActinosynnema pretiosum subsp. auranticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsZhang, F. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31570056,31770068 China
CitationJournal: Chembiochem / Year: 2020
Title: Structural and Biochemical Insight into the Recruitment of Acyl Carrier Protein-Linked Extender Units in Ansamitocin Biosynthesis.
Authors: Zhang, F. / Ji, H. / Ali, I. / Deng, Z. / Bai, L. / Zheng, J.
History
DepositionOct 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase
B: Polyketide synthase
C: Polyketide synthase
D: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,13718
Polymers176,6624
Non-polymers1,47514
Water21,9421218
1
A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4874
Polymers44,1651
Non-polymers3213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16860 Å2
MethodPISA
2
B: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4874
Polymers44,1651
Non-polymers3213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16780 Å2
MethodPISA
3
C: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5825
Polymers44,1651
Non-polymers4164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-5 kcal/mol
Surface area16870 Å2
MethodPISA
4
D: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5825
Polymers44,1651
Non-polymers4164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.299, 100.778, 103.267
Angle α, β, γ (deg.)90.000, 113.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Polyketide synthase


Mass: 44165.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinosynnema pretiosum subsp. auranticum (bacteria)
Gene: AsmAT3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8KUH4*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-E5U / 2-methoxypropanedioic acid


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1218 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.2M K2HPO4 (pH 6) , 7% PEG 3350 (W/V)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.77→98.54 Å / Num. obs: 186560 / % possible obs: 97.37 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 3
Reflection shellResolution: 1.77→98.54 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 186560

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HG4

2hg4


Resolution: 1.77→98.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.669 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 9904 5 %RANDOM
Rwork0.1885 ---
obs0.1899 186560 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.58 Å2 / Biso mean: 20.072 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å2-0.36 Å2
2--2.12 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: final / Resolution: 1.77→98.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12426 0 86 1218 13730
Biso mean--30.86 25.85 -
Num. residues----1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912727
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212619
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.97217371
X-RAY DIFFRACTIONr_angle_other_deg0.684328698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35651676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.45520.948517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.073151890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.66215180
X-RAY DIFFRACTIONr_chiral_restr0.0860.22079
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02114487
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022881
LS refinement shellResolution: 1.767→1.813 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 709 -
Rwork0.263 13398 -
all-14107 -
obs--97.37 %

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