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- PDB-1j3n: Crystal Structure of 3-oxoacyl-(acyl-carrier protein) Synthase II... -

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Basic information

Entry
Database: PDB / ID: 1j3n
TitleCrystal Structure of 3-oxoacyl-(acyl-carrier protein) Synthase II from Thermus thermophilus HB8
Components3-oxoacyl-(acyl-carrier protein) synthase II
KeywordsTRANSFERASE / Condensing Enzymes / Fatty acid elongation / Acyl-carrier protein (ACP) / Beta-keto-ACP synthase (KAS) / Homodimer / Structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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 ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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
CITRIC ACID / 3-oxoacyl-[acyl-carrier-protein] synthase 2 / :
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBagautdinov, B. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of 3-oxoacyl-(acyl-carrier protein) synthase II from Thermus thermophilus HB8.
Authors: Bagautdinov, B. / Ukita, Y. / Miyano, M. / Kunishima, N.
History
DepositionFeb 10, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-(acyl-carrier protein) synthase II
B: 3-oxoacyl-(acyl-carrier protein) synthase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7414
Polymers86,5252
Non-polymers2162
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-59 kcal/mol
Surface area24850 Å2
MethodPISA
2
A: 3-oxoacyl-(acyl-carrier protein) synthase II
B: 3-oxoacyl-(acyl-carrier protein) synthase II
hetero molecules

A: 3-oxoacyl-(acyl-carrier protein) synthase II
B: 3-oxoacyl-(acyl-carrier protein) synthase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,4838
Polymers173,0504
Non-polymers4334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area14980 Å2
ΔGint-117 kcal/mol
Surface area47240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.067, 185.573, 62.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-717-

HOH

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Components

#1: Protein 3-oxoacyl-(acyl-carrier protein) synthase II


Mass: 43262.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: FabF / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q7SIC5, UniProt: Q5SL80*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.28 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.3
Details: PEG 4000, MAGNESIUM CHLORIDE, SODIUM CITRATE, pH 5.3, MICROBATCH, temperature 295K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118.0 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
350 mM1dropNaCl
425 %(w/v)PEG40001reservoir
50.05 M1reservoirMgCl2
60.100 mMsodium citrate1reservoirpH5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 276295 / Num. obs: 276295 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.095
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4619 / % possible all: 81.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 56133 / Redundancy: 4.8 %
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 81.1 % / Redundancy: 4.4 % / Num. unique obs: 4619

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E5M

1e5m


Resolution: 2→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The electron density is continuous but poor for sidechain atoms of residues: K30A, R62A, K63A, E64A, R66A, K89A, E91A, R204A, K245A, K246A, K385A, K63B, E64B, R66B, E91B, K215B, K246B, ...Details: The electron density is continuous but poor for sidechain atoms of residues: K30A, R62A, K63A, E64A, R66A, K89A, E91A, R204A, K245A, K246A, K385A, K63B, E64B, R66B, E91B, K215B, K246B, E273B, R318B, K325B, R326B, E367B, K385B
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 2850 5.1 %RANDOM
Rwork0.21 ---
all-57573 --
obs-56133 97.5 %-
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2--5.25 Å20 Å2
3----7.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6080 0 14 462 6556
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2-2.090.323170.28358000.01886.2
2.09-2.20.2883410.24865940.01697.8
2.2-2.340.28183330.236367110.01598.6
2.34-2.520.27523600.222267270.01599.3
2.52-2.770.27273620.220967590.01499.4
2.77-3.170.26683690.218767720.01499.2
3.17-40.25973860.195568240.01399.2
4-300.21743840.182371210.01199.7
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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