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- PDB-6mhp: Crystal structure of BaeC acyltransferase from bacillaene polyket... -

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Basic information

Entry
Database: PDB / ID: 6mhp
TitleCrystal structure of BaeC acyltransferase from bacillaene polyketide synthase in Bacillus amyloliquefaciens
ComponentsMalonyl CoA-acyl carrier protein transacylase
KeywordsTRANSFERASE / acyltransferase / polyketide assembly line / bacillaene
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity
Similarity search - Function
Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMeinke, J.L. / Keatinge-Clay, A.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106112 United States
CitationJournal: To Be Published
Title: BaeC crystal structure
Authors: Keatinge-Clay, A.T. / Meinke, J.L.
History
DepositionSep 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: Malonyl CoA-acyl carrier protein transacylase


Theoretical massNumber of molelcules
Total (without water)34,9901
Polymers34,9901
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.069, 50.142, 111.455
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 Malonyl CoA-acyl carrier protein transacylase


Mass: 34989.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: baeC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q1RS80, [acyl-carrier-protein] S-malonyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.84 Å3/Da / Density % sol: 33.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium formate, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 27508 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.819 / Rmerge(I) obs: 0.074 / Net I/σ(I): 35.6
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.713 / Num. unique obs: 1347 / CC1/2: 0.819 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGI

3rgi


Resolution: 1.73→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23034 1399 5.1 %RANDOM
Rwork0.1979 ---
obs0.19953 26244 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 0 62 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192264
X-RAY DIFFRACTIONr_bond_other_d00.022145
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9463054
X-RAY DIFFRACTIONr_angle_other_deg3.66334935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76824.404109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8415396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6181511
X-RAY DIFFRACTIONr_chiral_restr0.1360.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022585
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02540
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_it2.4562.7661123
X-RAY DIFFRACTIONr_mcbond_other2.4562.7651122
X-RAY DIFFRACTIONr_mcangle_it3.24.1441402
X-RAY DIFFRACTIONr_mcangle_other3.1994.1451403
X-RAY DIFFRACTIONr_scbond_it4.4593.321141
X-RAY DIFFRACTIONr_scbond_other4.4583.3221142
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6544.7611653
X-RAY DIFFRACTIONr_long_range_B_refined7.63322.7172541
X-RAY DIFFRACTIONr_long_range_B_other7.63722.6662523
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 107 -
Rwork0.243 1909 -
obs--99.12 %

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