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- PDB-6l3n: Crystal Structure of the acyltransferase domain from the third mo... -

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Basic information

Entry
Database: PDB / ID: 6l3n
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


fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Alpha-Beta Plaits - #3290 / : / Polyketide synthase dehydratase N-terminal domain / : / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : ...Alpha-Beta Plaits - #3290 / : / 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, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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
METHYLMALONIC ACID / PHOSPHATE ION / Polyketide synthase
Similarity search - Component
Biological speciesActinosynnema pretiosum subsp. auranticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsZhang, F. / Zheng, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)31570056 China
National Science Foundation (China)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 9, 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)183,08218
Polymers181,6724
Non-polymers1,41114
Water22,0861226
1
A: polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7234
Polymers45,4181
Non-polymers3053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16820 Å2
MethodPISA
2
B: polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7234
Polymers45,4181
Non-polymers3053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16770 Å2
MethodPISA
3
C: polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8185
Polymers45,4181
Non-polymers4004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-5 kcal/mol
Surface area16790 Å2
MethodPISA
4
D: polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8185
Polymers45,4181
Non-polymers4004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.803, 100.094, 103.152
Angle α, β, γ (deg.)90.000, 113.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
polyketide synthase


Mass: 45417.898 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: A0A1U9Y7T8*PLUS
#2: Chemical
ChemComp-DXX / METHYLMALONIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1226 / 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 / 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: 1.83→98.11 Å / Num. obs: 166143 / % possible obs: 97.94 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 3
Reflection shellResolution: 1.83→50 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 25349

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HG4

2hg4


Resolution: 1.83→98.11 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.201 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 8752 5 %RANDOM
Rwork0.1895 ---
obs0.1908 166143 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.66 Å2 / Biso mean: 20.048 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å2-0.28 Å2
2--2.42 Å20 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 1.83→98.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12426 0 82 1226 13734
Biso mean--28.77 26.13 -
Num. residues----1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912716
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212462
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.97117356
X-RAY DIFFRACTIONr_angle_other_deg0.654328412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13351674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.60120.93516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.823151888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.66615180
X-RAY DIFFRACTIONr_chiral_restr0.080.22078
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02114412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022728
LS refinement shellResolution: 1.83→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 623 -
Rwork0.276 12098 -
all-12721 -
obs--97.94 %

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