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- PDB-4jrh: Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Vi... -

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Basic information

Entry
Database: PDB / ID: 4jrh
TitleCrystal structure of beta-ketoacyl-ACP synthase II (FabF) from Vibrio Cholerae (space group P43) at 2.2 Angstrom
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / FabF
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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 ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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
ACETATE ION / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsHou, J. / Chruszcz, M. / Shabalin, I.G. / Zheng, H. / Cooper, D.R. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _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 1.3Feb 28, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1714
Polymers87,0532
Non-polymers1182
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-46 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.547, 124.547, 64.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 3 - 413 / Label seq-ID: 6 - 416

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2 / 3-oxoacyl-[acyl-carrier-protein] synthase II / Beta-ketoacyl-ACP synthase II / KAS II


Mass: 43526.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fabF, VC2019, VC_2019 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9KQH9, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis-Tris, 0.2M NaAc, 20% PEG 3350, pH 6.5, vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2012 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→27 Å / Num. obs: 50309 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 24.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2494 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1853 / WRfactor Rwork: 0.1545 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.869 / SU B: 4.846 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1993 / SU Rfree: 0.1625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 2562 5.1 %RANDOM
Rwork0.1673 ---
obs0.1689 50286 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.24 Å2 / Biso mean: 40.1993 Å2 / Biso min: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å2-0 Å2-0 Å2
2--1.3 Å2-0 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5974 0 8 322 6304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196105
X-RAY DIFFRACTIONr_bond_other_d0.0040.025842
X-RAY DIFFRACTIONr_angle_refined_deg1.491.968243
X-RAY DIFFRACTIONr_angle_other_deg0.987313433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54724.359234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.211151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8271534
X-RAY DIFFRACTIONr_chiral_restr0.0870.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027109
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021325
Refine LS restraints NCS

Ens-ID: 1 / Number: 24346 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 184 -
Rwork0.244 3444 -
all-3628 -
obs--98.11 %

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