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- PDB-4ewg: Crystal structure of a Beta-ketoacyl synthase from Burkholderia p... -

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Basic information

Entry
Database: PDB / ID: 4ewg
TitleCrystal structure of a Beta-ketoacyl synthase from Burkholderia phymatum STM815
ComponentsBeta-ketoacyl synthase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


transferase activity
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. / 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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 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
IMIDAZOLE / Beta-ketoacyl synthase
Similarity search - Component
Biological speciesBurkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-ketoacyl synthase
B: Beta-ketoacyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,72710
Polymers88,2172
Non-polymers5108
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-41 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.410, 60.940, 99.680
Angle α, β, γ (deg.)90.000, 95.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-ketoacyl synthase


Mass: 44108.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phymatum (bacteria) / Strain: STM815 / Gene: Bphy_0703 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2JEW3
#2: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 45.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Internal tracking number 230204c7. JCSG Core Suite IV well c7. 0.1M Imidazole Buffer pH 8.0, 10.0% w/v PEG8,000, 20% ethylene glycol. BuphA.00113.a.A1 ps01343 24.9mg/ml, vapor diffusion, ...Details: Internal tracking number 230204c7. JCSG Core Suite IV well c7. 0.1M Imidazole Buffer pH 8.0, 10.0% w/v PEG8,000, 20% ethylene glycol. BuphA.00113.a.A1 ps01343 24.9mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→49.64 Å / Num. all: 37978 / Num. obs: 36898 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 27.255 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.25-2.310.3893.78138247988.5
2.31-2.370.3274.48979263496.3
2.37-2.440.2884.98674254296.8
2.44-2.520.2655.38530248597.8
2.52-2.60.2465.78412243597.5
2.6-2.690.2116.87977233797.5
2.69-2.790.1927.47973229097.6
2.79-2.90.1638.77735221998.4
2.9-3.030.13710.17429211998.3
3.03-3.180.10912.57098201798.6
3.18-3.350.08515.66850193898.8
3.35-3.560.06619.96382182298.2
3.56-3.80.04826.65768169997.5
3.8-4.110.04329.55483160098.2
4.11-4.50.03634.55180149398.7
4.5-5.030.037334693135098.8
5.03-5.810.05124.64156118498.7
5.81-7.120.04925.83555101598.8
7.12-10.060.02842272580898.5
10.060.0256.3135043293.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.81 Å
Translation2.5 Å41.81 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3HO9

3ho9


Resolution: 2.25→49.64 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.348 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.36 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1819 4.9 %RANDOM
Rwork0.19 ---
all0.192 37978 --
obs0.192 36892 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20.95 Å2
2---0.29 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 34 321 6403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196204
X-RAY DIFFRACTIONr_bond_other_d0.0050.024070
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9498423
X-RAY DIFFRACTIONr_angle_other_deg1.10239857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38823.189254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29115928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8681547
X-RAY DIFFRACTIONr_chiral_restr0.0750.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217125
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021332
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 135 -
Rwork0.353 2261 -
all-2396 -
obs--88.09 %
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)
11.1998-0.38650.31171.861-0.06260.20140.08590.1016-0.0646-0.1164-0.00560.31360.0822-0.1006-0.08030.0488-0.055-0.05150.14890.07580.09494.094716.852463.7182
20.72290.19970.18050.6609-0.25320.5352-0.02860.19260.0142-0.1670.07730.07450.0847-0.0156-0.04870.06590.0067-0.00180.08270.02710.023519.850723.758958.1192
30.6813-0.04160.06921.2241-0.1980.39890.0229-0.01190.0107-0.0586-0.0060.0550.1002-0.0844-0.01690.0341-0.00660.00360.0610.040.044714.834519.704669.0152
40.7413-0.10750.16811.07410.06620.62140.0367-0.1204-0.06620.04980.04680.17230.137-0.1558-0.08340.0405-0.01820.00790.07330.06650.08834.748212.931978.2083
51.22110.0759-0.60190.77380.04760.87180.037-0.0838-0.12590.1066-0.0411-0.15030.00570.16340.00410.03170.021-0.00860.07880.0380.075144.795929.473677.7089
60.61460.2753-0.04930.5986-0.19070.50060.0231-0.0686-0.02080.0487-0.0268-0.02960.0580.06420.00370.03490.03160.00730.05250.02450.022233.839325.982276.4093
72.124-0.15630.73292.2285-1.5751.30070.1743-0.0260.17340.1966-0.08880.1854-0.07590.0697-0.08540.06750.02320.02970.0807-0.040.048725.562737.622287.1275
80.82380.037-0.31111.3563-0.2971.2010.0451-0.05510.1720.086-0.04890.0345-0.1530.070.00380.03970.00430.01590.01870.00130.051734.469747.539679.2109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 39
2X-RAY DIFFRACTION2A40 - 134
3X-RAY DIFFRACTION3A135 - 245
4X-RAY DIFFRACTION4A246 - 408
5X-RAY DIFFRACTION5B2 - 67
6X-RAY DIFFRACTION6B68 - 240
7X-RAY DIFFRACTION7B241 - 272
8X-RAY DIFFRACTION8B273 - 408

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