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- PDB-4rl1: Structural and functional analysis of a loading acyltransferase f... -

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Basic information

Entry
Database: PDB / ID: 4rl1
TitleStructural and functional analysis of a loading acyltransferase from the avermectin modular polyketide synthase
ComponentsType I polyketide synthase AVES 1
KeywordsTRANSFERASE / hydrolase / ferredoxin-like fold / acyltransferase
Function / homology
Function and homology information


phosphopantetheine binding / antibiotic biosynthetic process / transferase activity
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / 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 / Phosphopantetheine attachment site / Thiolase-like / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type I polyketide synthase AVES 1
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, F. / Wang, Y. / Zheng, J.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Structural and functional analysis of the loading acyltransferase from avermectin modular polyketide synthase.
Authors: Wang, F. / Wang, Y. / Ji, J. / Zhou, Z. / Yu, J. / Zhu, H. / Su, Z. / Zhang, L. / Zheng, J.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type I polyketide synthase AVES 1


Theoretical massNumber of molelcules
Total (without water)39,7541
Polymers39,7541
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.210, 74.290, 82.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type I polyketide synthase AVES 1


Mass: 39753.891 Da / Num. of mol.: 1 / Fragment: UNP residues 1-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: ATCC 31267 / Gene: aveA1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q79ZN1, [acyl-carrier-protein] S-malonyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.82 Å3/Da / Density % sol: 32.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.75
Details: 3.4 M sodium formate, pH 6.75, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97891 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 20229 / Num. obs: 20108 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2-2.114.90.2098.12902199.9
6-314.10.05622.5650190

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERMRphasing
REFMAC5.8.0049refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HG4

2hg4


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.751 / SU ML: 0.138 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24155 1022 5.1 %RANDOM
Rwork0.20788 ---
obs0.20968 19000 99.01 %-
all-19191 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.141 Å2
Baniso -1Baniso -2Baniso -3
1--2.9 Å20 Å2-0 Å2
2---1.46 Å20 Å2
3---4.36 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 0 58 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192446
X-RAY DIFFRACTIONr_bond_other_d00.022362
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.973347
X-RAY DIFFRACTIONr_angle_other_deg0.70335412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9585316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02222.47497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38915368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1651524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
X-RAY DIFFRACTIONr_mcbond_it1.9791.4481270
X-RAY DIFFRACTIONr_mcbond_other1.9621.4461269
X-RAY DIFFRACTIONr_mcangle_it2.9122.161584
X-RAY DIFFRACTIONr_mcangle_other2.9112.1621585
X-RAY DIFFRACTIONr_scbond_it3.1341.8251176
X-RAY DIFFRACTIONr_scbond_other3.1331.8261177
X-RAY DIFFRACTIONr_scangle_other4.5832.6091764
X-RAY DIFFRACTIONr_long_range_B_refined6.66313.98310728
X-RAY DIFFRACTIONr_long_range_B_other6.66313.95510709
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 74 -
Rwork0.276 1413 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: -22.9699 Å / Origin y: -0.3675 Å / Origin z: -2.4362 Å
111213212223313233
T0.1259 Å2-0.0043 Å20.0027 Å2-0.106 Å20.0116 Å2--0.0096 Å2
L0.9265 °20.0767 °20.0056 °2-0.3673 °20.0538 °2--0.0547 °2
S-0.0184 Å °-0.0514 Å °0.0551 Å °-0.0381 Å °0.0071 Å °0.0415 Å °0.0436 Å °0.0366 Å °0.0112 Å °

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