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- PDB-3lrf: Crystal structure of beta-ketoacyl synthase from brucella melitensis -

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Basic information

Entry
Database: PDB / ID: 3lrf
TitleCrystal structure of beta-ketoacyl synthase from brucella melitensis
ComponentsBeta-ketoacyl synthase
KeywordsTRANSFERASE / SSGCID / NIH / NIAID / SBRI / UW / EMERALD BIOSTRUCTURES / BETA-KETOACYL SYNTHASE / BRUCELLA MELITENSIS / Acyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAbendroth, J. / Edwards, T. / Staker, B. / 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
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
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 1.3Jul 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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.4Sep 6, 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

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Assembly

Deposited unit
A: Beta-ketoacyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6662
Polymers45,6431
Non-polymers231
Water8,881493
1
A: Beta-ketoacyl synthase
hetero molecules

A: Beta-ketoacyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3334
Polymers91,2872
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5740 Å2
ΔGint-43 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.480, 83.270, 72.870
Angle α, β, γ (deg.)90.00, 120.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-ketoacyl synthase


Mass: 45643.273 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE; BRABA.00113.A AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 52414 / Num. obs: 51415 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 18.47 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 34.19
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3853 / % possible all: 91.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1dd8 modified with CCP4 program CHAINSAW

1dd8


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.294 / SU ML: 0.037 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.158 2613 5.1 %RANDOM
Rwork0.129 ---
all0.13 52414 --
obs0.13 51415 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20.05 Å2
2--0.29 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3091 0 1 493 3585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223155
X-RAY DIFFRACTIONr_bond_other_d0.0010.022113
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9544287
X-RAY DIFFRACTIONr_angle_other_deg0.87935163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98723.926135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79215526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0521523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
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_it0.7421.52046
X-RAY DIFFRACTIONr_mcbond_other0.2191.5854
X-RAY DIFFRACTIONr_mcangle_it1.29123283
X-RAY DIFFRACTIONr_scbond_it2.16731109
X-RAY DIFFRACTIONr_scangle_it3.5374.5991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 170 -
Rwork0.205 3356 -
obs--91.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.28230.0649-0.06350.1782-0.06880.1634-0.0220.0278-0.0201-0.00840.019-0.03690.01010.00940.0030.0142-0.00330.01450.0175-0.00560.022429.497-2.31622.828
20.35060.1015-0.16140.40210.08910.4181-0.00620.1260.0387-0.04770.01110.0398-0.0221-0.0399-0.00490.02-0.0049-0.00050.05870.01530.010219.4548.5168.611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 248
2X-RAY DIFFRACTION2A250 - 407

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