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- PDB-6hp1: Crystal Structure of the O-Methyltransferase from the trans-AT PK... -

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Basic information

Entry
Database: PDB / ID: 6hp1
TitleCrystal Structure of the O-Methyltransferase from the trans-AT PKS multienzyme C0ZGQ3 of Brevibacillus brevis
ComponentsPutative polyketide synthase
KeywordsTRANSFERASE / Polyketide / PKS / natural product / biosynthesis
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Mycolic acid cyclopropane synthetase / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase ...Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Mycolic acid cyclopropane synthetase / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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 / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ETHYL MERCURY ION / Putative polyketide synthase
Similarity search - Component
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJakob, R.P. / Felber, P. / Demyanenko, Y. / Delbart, F. / Maier, T.
CitationJournal: To Be Published
Title: Structural and Functional Analysis of an O-Methyltransferase from the trans-AT PKS biosynthesis pathway
Authors: Jakob, R.P. / Felber, P. / Demyanenko, Y. / Delbart, F. / Maier, T.
History
DepositionSep 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3885
Polymers39,4701
Non-polymers9194
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-5 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.613, 71.760, 61.192
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative polyketide synthase /


Mass: 39469.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (strain 47 / JCM 6285 / NBRC 100599) (bacteria)
Gene: BBR47_39850 / Plasmid: pBX-NH3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0ZGQ3
#2: Chemical
ChemComp-EMC / ETHYL MERCURY ION / Ethylmercury


Mass: 229.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES 7.17 pH , 14 %w/v PEG 20K; soaked with 10mM Thiomersal for 10min

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 1.9→45.737 Å / Num. obs: 29477 / % possible obs: 99.56 % / Redundancy: 19.3 % / CC1/2: 1 / Rmerge(I) obs: 0.296 / Rpim(I) all: 0.069 / Rrim(I) all: 0.312 / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 15 % / Rmerge(I) obs: 2.111 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2915 / CC1/2: 0.757 / Rpim(I) all: 0.574 / Rrim(I) all: 2.265 / % possible all: 98.45

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→45.737 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.34
RfactorNum. reflection% reflection
Rfree0.2045 1413 4.79 %
Rwork0.1731 --
obs0.1746 29477 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 12 234 2650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012494
X-RAY DIFFRACTIONf_angle_d0.8853369
X-RAY DIFFRACTIONf_dihedral_angle_d14.8391516
X-RAY DIFFRACTIONf_chiral_restr0.059372
X-RAY DIFFRACTIONf_plane_restr0.007436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.2971490.26922766X-RAY DIFFRACTION98
1.9679-2.04670.23541380.22182783X-RAY DIFFRACTION99
2.0467-2.13990.22051330.18562787X-RAY DIFFRACTION99
2.1399-2.25270.19341380.17672803X-RAY DIFFRACTION100
2.2527-2.39380.18931300.17112788X-RAY DIFFRACTION100
2.3938-2.57860.19341300.15782817X-RAY DIFFRACTION100
2.5786-2.83810.17741520.16532792X-RAY DIFFRACTION100
2.8381-3.24870.17491560.17152829X-RAY DIFFRACTION100
3.2487-4.09260.21351270.15392848X-RAY DIFFRACTION100
4.0926-45.75040.21461600.17372851X-RAY DIFFRACTION100
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)
12.7482-0.40610.4711.9508-0.2951.1397-0.1147-0.06480.17920.09880.0905-0.2389-0.00170.16520.030.15850.0106-0.0230.2037-0.00890.168424.630647.479637.3799
22.30940.2786-1.64520.1828-0.1483.72160.1364-0.63120.56610.681-0.03790.0997-0.2130.1766-0.07160.53230.00240.05610.3878-0.0910.34177.036958.393249.2768
31.34030.26290.48092.35450.57361.3971-0.0840.1801-0.0104-0.17610.10750.0535-0.01070.1417-0.03690.19440.0058-0.0050.21860.01090.147417.966242.172328.7685
41.5246-0.33120.17221.480.47191.372-0.0292-0.22890.08930.15390.00410.0820.0372-0.19620.02320.1839-0.0178-0.00520.2243-0.00050.19524.821342.040940.6211
51.66921.23740.63432.13281.02812.53670.1842-0.3471-0.12940.3339-0.2303-0.05320.5111-0.06230.00250.33710.0156-0.04330.26640.04740.24320.382830.919248.1144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 166 through 249 )
2X-RAY DIFFRACTION2chain 'A' and (resid 250 through 281 )
3X-RAY DIFFRACTION3chain 'A' and (resid 282 through 338 )
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 165 )

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