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- PDB-4jv3: Crystal structure of beta-ketoacyl synthase from Brucella meliten... -

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Basic information

Entry
Database: PDB / ID: 4jv3
TitleCrystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with platencin
ComponentsBeta-ketoacyl synthase
KeywordsTransferase/Antibiotic / SSGCID / beta-ketoacyl synthase / platencin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Transferase-Antibiotic complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N32 / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Proteins / Year: 2020
Title: Structural characterization of beta-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites.
Authors: Patterson, E.I. / Nanson, J.D. / Abendroth, J. / Bryan, C. / Sankaran, B. / Myler, P.J. / Forwood, J.K.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Structure summary
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 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: Beta-ketoacyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1492
Polymers45,7231
Non-polymers4251
Water7,800433
1
A: Beta-ketoacyl synthase
hetero molecules

A: Beta-ketoacyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2984
Polymers91,4472
Non-polymers8512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5890 Å2
ΔGint-43 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.160, 84.480, 74.020
Angle α, β, γ (deg.)90.000, 120.810, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a dimer generated from the monomer in the asymmetric unit by the operation: -X+1, Y, -Z+1

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Components

#1: Protein Beta-ketoacyl synthase


Mass: 45723.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: fabB, BAB1_2173 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2YQQ9, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-N32 / 2,4-dihydroxy-3-({3-[(2S,4aS,8S,8aR)-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid / Platencin


Mass: 425.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MD PACT screen, H2: 20% PEG 3350, 100mM BisTrisPropane pH 8.5, 200mM Na-bromide; tray 233841 f11, BrabA.00113.a at 23 mg/ml, 2.5mM platencin, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 7, 2013 / Details: Rigaku VariMax
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 45545 / Num. obs: 44869 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 20.929 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 47.79
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.740.1877.52132353278196.8
1.74-1.790.169.35179853221199.6
1.79-1.840.12311.52186043161199.4
1.84-1.90.13112.15182082974196.1
1.9-1.960.09620.09183762927197.9
1.96-2.030.07122.69210852808198
2.03-2.110.05731.22261252808199.6
2.11-2.190.05538.91308912641198
2.19-2.290.06247.26304372539197.8
2.29-2.40.04751.36323252397196.6
2.4-2.530.03760.66330862314199.4
2.53-2.690.03767.93328382217199.9
2.69-2.870.03179.14361002096199.5
2.87-3.10.02988.94361171933199.6
3.1-3.40.02797.42338241811199.5
3.4-3.80.029103.47282011610199.6
3.8-4.390.024115.77268361438199
4.39-5.380.022122.08226181213199.5
5.38-7.60.024114.6317567947199.5
7.6-500.023123.449211536198

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3LRF

3lrf


Resolution: 1.7→42.28 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.159 / WRfactor Rwork: 0.1335 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9088 / SU B: 2.772 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0868 / SU Rfree: 0.0843 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 2264 5 %RANDOM
Rwork0.1425 ---
all0.14382 45545 --
obs0.1438 44869 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.4 Å2 / Biso mean: 16.929 Å2 / Biso min: 3.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.35 Å2
2---0.1 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 31 433 3469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193141
X-RAY DIFFRACTIONr_bond_other_d0.0010.022910
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9554273
X-RAY DIFFRACTIONr_angle_other_deg0.7662.9926692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50323.712132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63715498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4021524
X-RAY DIFFRACTIONr_chiral_restr0.090.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023665
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02711
X-RAY DIFFRACTIONr_mcbond_it0.7360.9911644
X-RAY DIFFRACTIONr_mcbond_other0.7340.991643
X-RAY DIFFRACTIONr_mcangle_it1.191.4852058
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 194 -
Rwork0.15 3077 -
all-3271 -
obs-3077 96.98 %
Refinement TLS params.Method: refined / Origin x: 25.63 Å / Origin y: 2.007 Å / Origin z: 17.864 Å
111213212223313233
T0.0166 Å2-0.0138 Å20.012 Å2-0.0239 Å2-0.0076 Å2--0.0222 Å2
L0.4527 °20.0493 °2-0.1393 °2-0.3926 °2-0.0426 °2--0.3159 °2
S-0.0396 Å °0.0937 Å °-0.0187 Å °-0.0662 Å °0.0291 Å °-0.0235 Å °0.0052 Å °-0.0066 Å °0.0105 Å °

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