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- PDB-6a9n: Crystal structure of KAS III from Propionibacterium acnes -

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Basic information

Entry
Database: PDB / ID: 6a9n
TitleCrystal structure of KAS III from Propionibacterium acnes
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / ketoacyl-ACP synthase
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 3-oxoacyl-[acyl-carrier-protein] synthase 3
Similarity search - Component
Biological speciesCutibacterium acnes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.099 Å
AuthorsLee, W.C. / Cheon, D. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)MSIP-2016R1A2B2008543 Korea, Republic Of
CitationJournal: to be published
Title: Crystal structure of KAS III from Propionibacterium acnes
Authors: Cheon, D. / Lee, W.C. / Kim, Y.
History
DepositionJul 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1679
Polymers70,8402
Non-polymers3277
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-31 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.518, 105.518, 326.933
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-699-

HOH

21A-716-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III


Mass: 35420.027 Da / Num. of mol.: 2 / Mutation: C122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutibacterium acnes (bacteria) / Gene: fabH, B1B09_02220 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2B7IGT3, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.71 Å3/Da / Density % sol: 66.83 % / Mosaicity: 0.271 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 4M potassium formate, 0.1M BIS-TRIS propane pH 9, PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 64032 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 16.38 Å2 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.046 / Rrim(I) all: 0.173 / Χ2: 2.225 / Net I/σ(I): 8.3 / Num. measured all: 894357
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1814.50.5762530.9590.1530.5911.543100
2.18-2.2614.10.57262740.9630.1590.5942.058100
2.26-2.3714.50.44162750.980.1190.4571.617100
2.37-2.4914.50.34462950.9860.0930.3561.603100
2.49-2.6514.50.29263380.9870.0790.3031.691100
2.65-2.8514.40.21363390.9920.0580.2211.931100
2.85-3.1414.30.14563710.9960.040.1512.09100
3.14-3.5913.90.10864360.9970.030.1122.829100
3.59-4.5212.70.08765280.9970.0250.093.947100
4.52-5012.50.06169230.9990.0180.0643.18399.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 2.099→35.011 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 1929 3.12 %
Rwork0.1767 --
obs0.1777 61907 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→35.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 12 400 5344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075025
X-RAY DIFFRACTIONf_angle_d0.8266833
X-RAY DIFFRACTIONf_dihedral_angle_d3.2823020
X-RAY DIFFRACTIONf_chiral_restr0.054800
X-RAY DIFFRACTIONf_plane_restr0.006890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0987-2.15120.25261370.18574150X-RAY DIFFRACTION96
2.1512-2.20940.21671300.18294171X-RAY DIFFRACTION96
2.2094-2.27440.36591190.27653541X-RAY DIFFRACTION82
2.2744-2.34780.25241360.18744182X-RAY DIFFRACTION96
2.3478-2.43170.20381310.18474202X-RAY DIFFRACTION96
2.4317-2.5290.2391370.18174238X-RAY DIFFRACTION97
2.529-2.6440.22841320.1914238X-RAY DIFFRACTION97
2.644-2.78340.24741410.1834313X-RAY DIFFRACTION98
2.7834-2.95770.22381400.18364331X-RAY DIFFRACTION99
2.9577-3.18590.1931420.17784400X-RAY DIFFRACTION99
3.1859-3.50630.21571420.17544423X-RAY DIFFRACTION99
3.5063-4.0130.17631400.15144432X-RAY DIFFRACTION99
4.013-5.05350.14981480.13424554X-RAY DIFFRACTION100
5.0535-35.01570.17791540.18614803X-RAY DIFFRACTION99

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