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- PDB-6j0u: Crystal Structure of the acyltransferase domain from the third mo... -

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Basic information

Entry
Database: PDB / ID: 6j0u
TitleCrystal Structure of the acyltransferase domain from the third module of the ansamitocin polyketide synthase
ComponentsType 1 modular polyketide synthase
KeywordsTRANSFERASE / acyltransferase / methoxymalonyl-ACP / polyketide
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily ...Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Polyketide synthase
Similarity search - Component
Biological speciesActinosynnema pretiosum subsp. auranticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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
DepositionDec 26, 2018Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type 1 modular polyketide synthase
B: Type 1 modular polyketide synthase
C: Type 1 modular polyketide synthase
D: Type 1 modular polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,36310
Polymers196,7934
Non-polymers5706
Water22,9511274
1
A: Type 1 modular polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2932
Polymers49,1981
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17070 Å2
MethodPISA
2
B: Type 1 modular polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2932
Polymers49,1981
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16820 Å2
MethodPISA
3
C: Type 1 modular polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3883
Polymers49,1981
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-5 kcal/mol
Surface area16970 Å2
MethodPISA
4
D: Type 1 modular polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3883
Polymers49,1981
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.728, 100.303, 103.409
Angle α, β, γ (deg.)90.00, 113.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Type 1 modular polyketide synthase


Mass: 49198.172 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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 1274 / Source method: isolated from a natural source / Formula: H2O

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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: 6.2 / Details: 0.2M K2HPO4 pH 6, 7% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 176984 / % possible obs: 98.56 % / Redundancy: 3.4 % / Net I/σ(I): 22
Reflection shellResolution: 1.79→1.84 Å

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Processing

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

2hg4


Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.906 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21863 8630 4.6 %RANDOM
Rwork0.18733 ---
obs0.1888 176984 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å2-0.54 Å2
2--2.91 Å20 Å2
3----1.19 Å2
Refinement stepCycle: 1 / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12426 0 30 1274 13730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912700
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212600
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.96817352
X-RAY DIFFRACTIONr_angle_other_deg0.691328657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30851682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.77721520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.551151896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.89515180
X-RAY DIFFRACTIONr_chiral_restr0.0870.22074
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02114510
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022890
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7162.0726716
X-RAY DIFFRACTIONr_mcbond_other2.7092.0726715
X-RAY DIFFRACTIONr_mcangle_it3.4853.0928390
X-RAY DIFFRACTIONr_mcangle_other3.4853.0938391
X-RAY DIFFRACTIONr_scbond_it4.7212.6185984
X-RAY DIFFRACTIONr_scbond_other4.5692.6045961
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5143.7038923
X-RAY DIFFRACTIONr_long_range_B_refined7.85727.71414968
X-RAY DIFFRACTIONr_long_range_B_other7.77226.97714382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 658 -
Rwork0.265 12370 -
obs--94.32 %

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