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- PDB-7vwk: The product template domain of AviM -

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Basic information

Entry
Database: PDB / ID: 7vwk
TitleThe product template domain of AviM
ComponentsPolyketide synthase
KeywordsANTIBIOTIC / iterative polyketide synthase / product template domain / C2-C7 cyclization
Function / homology
Function and homology information


polyketide biosynthetic process / organic cyclic compound biosynthetic process / 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, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain ...Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / 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 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Biological speciesStreptomyces viridochromogenes Tue57 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFeng, Y. / Yang, X. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070040 China
CitationJournal: Commun Biol / Year: 2022
Title: The Streptomyces viridochromogenes product template domain represents an evolutionary intermediate between dehydratase and aldol cyclase of type I polyketide synthases.
Authors: Feng, Y. / Yang, X. / Ji, H. / Deng, Z. / Lin, S. / Zheng, J.
History
DepositionNov 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase
B: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)54,4912
Polymers54,4912
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-8 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.679, 58.708, 82.502
Angle α, β, γ (deg.)90.000, 96.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyketide synthase /


Mass: 27245.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridochromogenes Tue57 (bacteria)
Gene: aviM / Production host: Escherichia coli (E. coli) / References: UniProt: O05170
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 1 M lithium chloride, 28% PEG 4000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→82.01 Å / Num. obs: 31071 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.445 / Num. unique obs: 1588

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.058 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1657 5.1 %RANDOM
Rwork0.2022 ---
obs0.2048 31071 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.99 Å2 / Biso mean: 49.743 Å2 / Biso min: 21.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å2-2.51 Å2
2--1.34 Å20 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 0 39 3732
Biso mean---41.06 -
Num. residues----500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193783
X-RAY DIFFRACTIONr_bond_other_d0.0010.023560
X-RAY DIFFRACTIONr_angle_refined_deg0.7831.9725188
X-RAY DIFFRACTIONr_angle_other_deg0.52638200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8515498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98922.922154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96915546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9651537
X-RAY DIFFRACTIONr_chiral_restr0.0590.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214294
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02735
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.28 103 -
Rwork0.272 2161 -
obs--92.86 %

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