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- PDB-3ou7: DhpI-SAM-HEP complex -

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Basic information

Entry
Database: PDB / ID: 3ou7
TitleDhpI-SAM-HEP complex
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / O-Methyltransferase / SAM / hydroxyethylphosphonic acid
Function / homology
Function and homology information


antibiotic biosynthetic process / methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2-hydroxyethyl)phosphonic acid / S-ADENOSYLMETHIONINE / SAM-dependent methyltransferase
Similarity search - Component
Biological speciesStreptomyces luridus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBae, B. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Characterization and structure of DhpI, a phosphonate O-methyltransferase involved in dehydrophos biosynthesis.
Authors: Lee, J.H. / Bae, B. / Kuemin, M. / Circello, B.T. / Metcalf, W.W. / Nair, S.K. / van der Donk, W.A.
History
DepositionSep 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
C: SAM-dependent methyltransferase
D: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,42912
Polymers98,4214
Non-polymers2,0088
Water9,620534
1
A: SAM-dependent methyltransferase
D: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2296
Polymers49,2112
Non-polymers1,0194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-4 kcal/mol
Surface area18430 Å2
MethodPISA
2
B: SAM-dependent methyltransferase
C: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2006
Polymers49,2112
Non-polymers9894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-2 kcal/mol
Surface area18840 Å2
MethodPISA
3
A: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
C: SAM-dependent methyltransferase
D: SAM-dependent methyltransferase
hetero molecules

A: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
C: SAM-dependent methyltransferase
D: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,85824
Polymers196,8428
Non-polymers4,01616
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area21810 Å2
ΔGint-7 kcal/mol
Surface area62790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.286, 167.286, 168.403
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
SAM-dependent methyltransferase


Mass: 24605.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces luridus (bacteria) / Gene: dhpI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7PC21
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-2HE / (2-hydroxyethyl)phosphonic acid


Mass: 126.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7O4P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 M Ammonium sulphate, 100 mM Tris-HCl pH=8.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97961 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 58659 / Num. obs: 58659 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 19.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5842 / % possible all: 96.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OU6

3ou6


Resolution: 2.3→41.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.967 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22708 2971 5.1 %RANDOM
Rwork0.17853 ---
obs0.18097 55673 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.111 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 0 130 534 7469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0217116
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.991.9489691
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6785849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33322.388381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.458151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9991585
X-RAY DIFFRACTIONr_chiral_restr0.1350.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215641
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.091.54261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01226815
X-RAY DIFFRACTIONr_scbond_it3.43132855
X-RAY DIFFRACTIONr_scangle_it5.34.52876
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 208 -
Rwork0.216 4112 -
obs--96.26 %

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