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- PDB-7vrs: The complex of Acyltransferase and Acyl Carrier Protein Domains f... -

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Basic information

Entry
Database: PDB / ID: 7vrs
TitleThe complex of Acyltransferase and Acyl Carrier Protein Domains from module 9 of Salinomycin Polyketide Synthase
Components(Type I modular polyketide synthase) x 2
KeywordsTRANSFERASE / complex / cis-acting / acyltransferase / acyl carrier protein
Function / homology
Function and homology information


macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / 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, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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 / GroES-like superfamily / 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
1,1'-butane-1,4-diylbis(1H-pyrrole-2,5-dione) / 4'-PHOSPHOPANTETHEINE / Type I modular polyketide synthase
Similarity search - Component
Biological speciesStreptomyces albus subsp. albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFeng, Y. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770068, 32070040 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase.
Authors: Feng, Y. / Zhang, F. / Huang, S. / Deng, Z. / Bai, L. / Zheng, J.
History
DepositionOct 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,2536
Polymers108,3993
Non-polymers8553
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.613, 102.061, 150.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Type I modular polyketide synthase


Mass: 48557.383 Da / Num. of mol.: 2 / Mutation: S190C, C298S, C347S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus subsp. albus (bacteria)
Gene: salAV / Production host: Escherichia coli (E. coli) / References: UniProt: H1ZZT7
#2: Protein Type I modular polyketide synthase


Mass: 11283.735 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus subsp. albus (bacteria)
Gene: salAV / Production host: Escherichia coli (E. coli) / References: UniProt: H1ZZT7
#3: Chemical ChemComp-ME9 / 1,1'-butane-1,4-diylbis(1H-pyrrole-2,5-dione)


Mass: 248.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Tris-HCl (pH 8.0), 0.4 M MgCl2, 0.2 M Na2SO4, 26% (v/v) PEG 3350
PH range: 7.6-8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 36632 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 12.6
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1793

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VT1

7vt1


Resolution: 2.6→47.38 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 19.63 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.584 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1816 5 %RANDOM
Rwork0.1859 ---
obs0.1878 34508 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 239.95 Å2 / Biso mean: 41.361 Å2 / Biso min: 15.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0 Å2-0 Å2
2--0.07 Å2-0 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 2.6→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7143 0 57 119 7319
Biso mean--59.74 33.77 -
Num. residues----974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137337
X-RAY DIFFRACTIONr_bond_other_d00.0176991
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.62210008
X-RAY DIFFRACTIONr_angle_other_deg1.2341.56815994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9385971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04121.078371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.318151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6041558
X-RAY DIFFRACTIONr_chiral_restr0.0630.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.020.028569
X-RAY DIFFRACTIONr_gen_planes_other0.010.021667
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 120 -
Rwork0.26 2385 -
all-2505 -
obs--94.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1681-0.15220.03790.3571-0.12060.48310.0247-0.03710.0315-0.052-0.0175-0.0001-0.01540.0225-0.00720.1018-0.0056-0.00870.02990.00010.0607-35.755228.183-6.4601
20.18810.2279-0.1850.5434-0.31840.3549-0.0135-0.02480.0090.0590.02790.06670.0113-0.0023-0.01440.0743-0.0130.01460.0586-0.00260.0598-57.078214.4722.1889
310.1053-0.74252.16180.5815-0.59371.0245-0.03070.2607-0.0268-0.0297-0.03780.11720.0453-0.0160.06850.0069-0.0070.02040.0521-0.06470.188-8.753934.2936-4.262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 444
2X-RAY DIFFRACTION2B1 - 444
3X-RAY DIFFRACTION3C2 - 87

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