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- PDB-6u0j: Crosslinked Crystal Structure of Malonyl-CoA Acyl Carrier Protein... -

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Basic information

Entry
Database: PDB / ID: 6u0j
TitleCrosslinked Crystal Structure of Malonyl-CoA Acyl Carrier Protein Transacylase, FabD, and Acyl Carrier Protein, AcpP
Components
  • Acyl carrier protein
  • Malonyl CoA-acyl carrier protein transacylase
KeywordsTRANSFERASE / MAT / AT / acyl transferase / alpha-beta hydrolase fold / AcpP / ACP / CP
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / acyl binding / lipid A biosynthetic process / lipid biosynthetic process / acyl carrier activity / phosphopantetheine binding / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding ...[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / acyl binding / lipid A biosynthetic process / lipid biosynthetic process / acyl carrier activity / phosphopantetheine binding / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / cytosol / cytoplasm
Similarity search - Function
Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / 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 / Acyl carrier protein (ACP) / Phosphopantetheine attachment site ...Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / 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 / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Chem-9EF / Acyl carrier protein / Acyl carrier protein / Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMindrebo, J.T. / Misson, L. / Davis, T.D. / Burkart, M.D. / Noel, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD.
Authors: Misson, L.E. / Mindrebo, J.T. / Davis, T.D. / Patel, A. / McCammon, J.A. / Noel, J.P. / Burkart, M.D.
History
DepositionAug 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malonyl CoA-acyl carrier protein transacylase
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,21711
Polymers42,3032
Non-polymers9149
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-14 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.150, 56.846, 99.874
Angle α, β, γ (deg.)90.000, 97.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Malonyl CoA-acyl carrier protein transacylase / MCT


Mass: 32741.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fabD, tfpA, b1092, JW1078 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AAI9, [acyl-carrier-protein] S-malonyltransferase
#2: Protein Acyl carrier protein / / ACP


Mass: 9561.419 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12 / DH10B) (bacteria)
Strain: K12 / DH10B / Gene: acpP, ECDH10B_1166 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B1XA04, UniProt: P0A6A8*PLUS

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Non-polymers , 4 types, 359 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26N3O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.7 % / Mosaicity: 0.46 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 % PEG 400, 0.1 M sodium cacodylate pH 6.5, and 2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44.73 Å / Num. obs: 32206 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 15.76 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.305 / Rpim(I) all: 0.122 / Rrim(I) all: 0.329 / Net I/σ(I): 7.2 / Num. measured all: 231636 / Scaling rejects: 136
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.779 / Num. unique obs: 2091 / CC1/2: 0.468 / Rpim(I) all: 0.732 / Rrim(I) all: 1.927 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.727 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 1665 5.17 %
Rwork0.1846 30527 -
obs0.1865 32192 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.54 Å2 / Biso mean: 22.2438 Å2 / Biso min: 2.57 Å2
Refinement stepCycle: final / Resolution: 1.9→44.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 57 350 3243
Biso mean--26.2 30.13 -
Num. residues----382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.95590.36471320.33732554100
1.9559-2.01910.28811420.25052548100
2.0191-2.09120.24481320.22972509100
2.0912-2.17490.25671510.20542495100
2.1749-2.27390.23721320.19532539100
2.2739-2.39380.22241500.18832517100
2.3938-2.54380.24511360.18392534100
2.5438-2.74020.27761300.18132572100
2.7402-3.01580.19661300.1812538100
3.0158-3.45210.21011390.16372543100
3.4521-4.34870.1951470.1442254699
4.3487-44.7270.15841440.15942632100

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