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- PDB-3ofk: Crystal structure of N-methyltransferase NodS from Bradyrhizobium... -

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Basic information

Entry
Database: PDB / ID: 3ofk
TitleCrystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in complex with S-adenosyl-l-homocysteine (SAH)
ComponentsNodulation protein SRoot nodule
KeywordsTRANSFERASE / NODS / N-METHYLTRANSFERASE / SAH / SAM / NOD FACTOR / NODULATION / NITROGEN FIXATION / SYMBIOSIS / alpha/beta structure / variant of Rossmann fold / SAM-dependent N-methyltransferase / S-adenosyl-L-methionine (SAM) / lipochitooligosaccharide / Methylation
Function / homology
Function and homology information


oligosaccharide biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
Nodulation protein S, NodS / SAM-dependent methyltransferase, NodS-like / Nodulation protein S (NodS) / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Nodulation protein S
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsCakici, O. / Sikorski, M. / Stepkowski, T. / Bujacz, G. / Jaskolski, M.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of NodS N-Methyltransferase from Bradyrhizobium japonicum in Ligand-Free Form and as SAH Complex.
Authors: Cakici, O. / Sikorski, M. / Stepkowski, T. / Bujacz, G. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Cloning, expression, purification, crystallization and preliminary X-ray analysis of NodS N-methyltransferase from Bradyrhizobium japonicum WM9
Authors: Cakici, O. / Sikorski, M. / Stepkowski, T. / Bujacz, G. / Jaskolski, M.
History
DepositionAug 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Nodulation protein S
B: Nodulation protein S
C: Nodulation protein S
D: Nodulation protein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1478
Polymers96,6104
Non-polymers1,5384
Water15,241846
1
A: Nodulation protein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5372
Polymers24,1521
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nodulation protein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5372
Polymers24,1521
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nodulation protein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5372
Polymers24,1521
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nodulation protein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5372
Polymers24,1521
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.01, 143.30, 75.85
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Nodulation protein S / Root nodule


Mass: 24152.400 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The crystallized protein has a heptapeptide tag (GIDPFTM-) attached at the N-terminus (residues -6 through 0). The first codon of the nodS sequence (gtg) has been translated in this NodS ...Details: The crystallized protein has a heptapeptide tag (GIDPFTM-) attached at the N-terminus (residues -6 through 0). The first codon of the nodS sequence (gtg) has been translated in this NodS protein as Val1, which is different from the Met1 residue occurring in NodS isolated from Bradyrhizobium japonicum WM9. The present protein is therefore a single-site variant of the natural polypeptide.
Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: WM9 / Gene: nodS / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODONPLUS(DE3)RIPL
References: UniProt: Q9AQ22, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 846 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT VAL1 IS THE FIRST RESIDUE OF THE PROTEIN SEQUENCE AND CORRESPONDS TO ...THE AUTHORS STATE THAT VAL1 IS THE FIRST RESIDUE OF THE PROTEIN SEQUENCE AND CORRESPONDS TO STANDARD TRANSLATION OF THE GTG CODON AS VALINE, EVEN THOUGH IN THE SEQUENCE DATABASE REFERENCE THIS POSITION IS OCCUPIED BY METHIONINE.

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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: 46.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG 8000, 5 mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 72827 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 5.04 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.6
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.331 / SU ML: 0.127 / Cross valid method: R-FREE / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23764 1165 1.6 %RANDOM
Rwork0.18965 ---
obs0.19048 70528 100 %-
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: 39.766 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.25 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6133 0 104 846 7083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0216352
X-RAY DIFFRACTIONr_bond_other_d0.0010.024298
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9688617
X-RAY DIFFRACTIONr_angle_other_deg0.997310390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88823.056301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.577151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1631569
X-RAY DIFFRACTIONr_chiral_restr0.1080.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021314
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_it1.0341.53912
X-RAY DIFFRACTIONr_mcbond_other0.2671.51589
X-RAY DIFFRACTIONr_mcangle_it1.8732.56284
X-RAY DIFFRACTIONr_scbond_it4.51252440
X-RAY DIFFRACTIONr_scangle_it6.8102333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.571 75 -
Rwork0.566 4441 -
obs--100 %
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)
12.4443-0.6246-0.3583.5339-0.27983.62560.07280.0195-0.0207-0.3817-0.0418-0.2369-0.29430.35-0.03090.247-0.028-0.00480.13240.02010.120128.98131.87445.768
22.8362-0.81370.09894.11430.50244.08470.07970.1828-0.1603-0.4376-0.07660.1847-0.313-0.1314-0.00310.2828-0.0119-0.08340.1886-0.00360.178121.2124.25335.11
33.59171.2421-1.292410.0619-5.81716.0753-0.11940.03880.13610.3829-0.1397-0.6938-0.50520.4840.25920.0709-0.0303-0.0610.2126-0.04430.211634.64530.1974.798
41.9318-0.4819-0.60754.2398-0.02593.427-0.0421-0.11190.06410.29650.12020.2855-0.1355-0.1529-0.07820.0350.03670.01310.07630.01530.123418.64527.70174.48
53.7085-0.4479-0.10382.80530.02593.15380.03190.1652-0.0112-0.0822-0.02450.04080.17150.0574-0.00750.0120.0047-0.0030.01010.00830.052828.4531.33770.677
62.23070.26560.42754.01621.35263.9991-0.0412-0.193-0.15460.26860.02340.30170.2795-0.30160.01770.047-0.04440.03830.14850.04750.172917.839-7.37578.567
73.6412-1.3390.10274.74-0.26512.26090.02980.4251-0.1478-0.1419-0.01720.23720.3107-0.3458-0.01250.2342-0.0681-0.0320.2147-0.06410.148614.353-18.36930.772
82.19610.67790.38543.6682-0.523.1619-0.02030.06310.06470.11790.0396-0.1348-0.00340.0212-0.01940.1946-0.0309-0.04380.1736-0.04380.117524.253-8.26839.694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 99
2X-RAY DIFFRACTION2A100 - 199
3X-RAY DIFFRACTION3B4 - 29
4X-RAY DIFFRACTION4B30 - 199
5X-RAY DIFFRACTION5C4 - 116
6X-RAY DIFFRACTION6C117 - 205
7X-RAY DIFFRACTION7D23 - 97
8X-RAY DIFFRACTION8D98 - 203

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