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- PDB-3u0f: The structure of Beta-ketoacyl synthase from Brucella melitensis ... -

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Basic information

Entry
Database: PDB / ID: 3u0f
TitleThe structure of Beta-ketoacyl synthase from Brucella melitensis bound to the fragment 7-hydroxycoumarin
ComponentsBeta-ketoacyl synthase
KeywordsTRANSFERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Beta-ketoacyl synthase
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-hydroxy-2H-chromen-2-one / METHANOL / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Direct phasing from previous structure / Resolution: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
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
Revision 1.2Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 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)43,9727
Polymers43,6521
Non-polymers3206
Water9,368520
1
A: Beta-ketoacyl synthase
hetero molecules

A: Beta-ketoacyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,94414
Polymers87,3042
Non-polymers64012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7200 Å2
ΔGint-93 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.560, 83.250, 73.810
Angle α, β, γ (deg.)90.000, 121.200, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

21A-538-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-ketoacyl synthase


Mass: 43652.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: BAB1_2173, fabB / Production host: Escherichia coli (E. coli)
References: UniProt: Q2YQQ9, beta-ketoacyl-[acyl-carrier-protein] synthase I

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Non-polymers , 5 types, 526 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-07L / 7-hydroxy-2H-chromen-2-one / 7-hydroxycoumarin / Umbelliferone


Mass: 162.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O3
#5: Chemical ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BrabA.00113.a at 22.94 mg/ml. 0.2M Sodium malonate, 0.1M Bis tris propane pH8.5, 20% PEG3350. BrabA.00113.a.A1 PW25441, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.25→39.275 Å / Num. obs: 109758 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.707 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.25-1.280.353.6327418766193
1.28-1.320.3094.5232680780796.7
1.32-1.360.2745.3834658761996.9
1.36-1.40.236.3233812739797.2
1.4-1.440.1947.5232945718697.5
1.44-1.490.1588.9532041697397.7
1.49-1.550.12810.6631166677497.9
1.55-1.610.10812.4929980651198.2
1.61-1.690.09513.9429125630898.4
1.69-1.770.08116.2127507595698.6
1.77-1.860.06918.6226494574298.7
1.86-1.980.05921.6425101542998.8
1.98-2.110.05224.5123654512799.1
2.11-2.280.04827.2322006476499.2
2.28-2.50.04428.9420330439599.4
2.5-2.80.04230.4718449398099.6
2.8-3.230.03932.2316341352599.6
3.23-3.950.03834.3113863299999.5
3.95-5.590.03635.4110749232299.2
5.590.03734.45741128397.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
REFMAC5.6.0117phasing
RefinementMethod to determine structure: Direct phasing from previous structure
Starting model: 3LRF

3lrf


Resolution: 1.25→39.275 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.1344 / WRfactor Rwork: 0.1216 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.947 / SU B: 0.859 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0356 / SU Rfree: 0.0323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1341 5497 5 %RANDOM
Rwork0.122 ---
obs0.1226 109671 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.3 Å2 / Biso mean: 10.2718 Å2 / Biso min: 3.13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.25→39.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 19 520 3555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193230
X-RAY DIFFRACTIONr_bond_other_d0.0020.022168
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9594395
X-RAY DIFFRACTIONr_angle_other_deg1.71335305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83823.852135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34315547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1571523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023720
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02664
X-RAY DIFFRACTIONr_rigid_bond_restr9.4935398
X-RAY DIFFRACTIONr_sphericity_free14.457598
X-RAY DIFFRACTIONr_sphericity_bonded3.87255751
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 381 -
Rwork0.175 7183 -
all-7564 -
obs--93.04 %

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