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- PDB-1ub7: The Crystal Analysis of Beta-Keroacyl-[Acyl Carrier Protein] Synt... -

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Basic information

Entry
Database: PDB / ID: 1ub7
TitleThe Crystal Analysis of Beta-Keroacyl-[Acyl Carrier Protein] Synthase III (FABH)From Thermus Thermophilus.
Components3-oxoacyl-[acyl-carrier protein] synthase
KeywordsTRANSFERASE / Fatty acid synthesis / Beta-Ketoacyl-ACP Synthase III / FABH / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 3
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsInagaki, E. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase III (Fabh) from Thermus Thermophilus
Authors: Inagaki, E. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H.
History
DepositionMar 31, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
B: 3-oxoacyl-[acyl-carrier protein] synthase
C: 3-oxoacyl-[acyl-carrier protein] synthase
D: 3-oxoacyl-[acyl-carrier protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,20614
Polymers138,2854
Non-polymers92110
Water5,891327
1
A: 3-oxoacyl-[acyl-carrier protein] synthase
B: 3-oxoacyl-[acyl-carrier protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4195
Polymers69,1432
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-41 kcal/mol
Surface area21820 Å2
MethodPISA
2
C: 3-oxoacyl-[acyl-carrier protein] synthase
D: 3-oxoacyl-[acyl-carrier protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7879
Polymers69,1432
Non-polymers6457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-40 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.586, 91.355, 149.436
Angle α, β, γ (deg.)90.00, 98.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-[acyl-carrier protein] synthase / Beta-Ketoacyl-ACP Synthase III


Mass: 34571.340 Da / Num. of mol.: 4 / Mutation: L290V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7SI99, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0M Ammonium Sulfate, 2% PEG 400, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2002 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.3→50 Å / Num. all: 66013 / Num. obs: 66013 / % possible obs: 97.8 % / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2 / % possible all: 91.3

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HNJ

1hnj


Resolution: 2.3→45.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 442324.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3168 5.1 %RANDOM
Rwork0.193 ---
obs0.193 62532 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.0002 Å2 / ksol: 0.358349 e/Å3
Displacement parametersBiso mean: 50.2 Å2
Baniso -1Baniso -2Baniso -3
1-19.71 Å20 Å26.65 Å2
2---7.66 Å20 Å2
3----12.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9716 0 60 327 10103
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.961
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.431.5
X-RAY DIFFRACTIONc_mcangle_it4.812
X-RAY DIFFRACTIONc_scbond_it5.442
X-RAY DIFFRACTIONc_scangle_it7.142.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 426 5 %
Rwork0.313 8033 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_OCYS_REP.PARAMPROTEIN_OCYS.TOP
X-RAY DIFFRACTION2GLYC.PARAMGLYC.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM

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