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

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Basic information

Entry
Database: PDB / ID: 4jrm
TitleCrystal structure of beta-ketoacyl-ACP synthase II (FabF) from Vibrio Cholerae (space group P212121) at 1.75 Angstrom
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Vibrio cholerae / FabF / beta-ketoacyl-(acyl carrier protein) synthase
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 O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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)
CitationJournal: To be Published
Title: Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Vibrio cholerae (space group P43) at 2.2 Angstrom
Authors: Hou, 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 / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_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 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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
D: 3-oxoacyl-[acyl-carrier-protein] synthase 2
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
C: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,4088
Polymers174,1064
Non-polymers3024
Water12,322684
1
D: 3-oxoacyl-[acyl-carrier-protein] synthase 2
C: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1123
Polymers87,0532
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-46 kcal/mol
Surface area25710 Å2
MethodPISA
2
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)87,2965
Polymers87,0532
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-49 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.543, 136.376, 168.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22B
13D
23C
14A
24B
15A
25C
16B
26C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETDA3 - 4146 - 417
21METMETAB3 - 4146 - 417
12METMETDA3 - 4146 - 417
22METMETBC3 - 4146 - 417
13ARGARGDA3 - 4136 - 416
23ARGARGCD3 - 4136 - 416
14METMETAB3 - 4146 - 417
24METMETBC3 - 4146 - 417
15ARGARGAB3 - 4136 - 416
25ARGARGCD3 - 4136 - 416
16ARGARGBC3 - 4136 - 416
26ARGARGCD3 - 4136 - 416

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 43526.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 (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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M sodium acetate, 25-28% PEG3350, 0.1 M Bis-Tris, 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: Oct 22, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 146834 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 40.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7210 / % possible all: 97.1

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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
Starting model: PDB ENTRY 1KAS

1kas


Resolution: 1.75→46.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2311 / WRfactor Rwork: 0.2003 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8255 / SU B: 3.473 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1377 / SU Rfree: 0.1256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 7353 5 %RANDOM
Rwork0.201 ---
obs0.2025 146142 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 94.01 Å2 / Biso mean: 34.8046 Å2 / Biso min: 16.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0 Å2
2---2.7 Å2-0 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11957 0 20 684 12661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912260
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211754
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.96116559
X-RAY DIFFRACTIONr_angle_other_deg1.191327041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04551669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82924.292473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.432152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3781571
X-RAY DIFFRACTIONr_chiral_restr0.0850.21859
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214273
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022666
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D241900.09
12A241900.09
21D246140.08
22B246140.08
31D240040.09
32C240040.09
41A244050.09
42B244050.09
51A245250.08
52C245250.08
61B242100.09
62C242100.09
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 546 -
Rwork0.326 10052 -
all-10598 -
obs--96.27 %

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