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- PDB-2e0n: Crystal structure of CbiL in complex with S-adenosylhomocysteine,... -

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Basic information

Entry
Database: PDB / ID: 2e0n
TitleCrystal structure of CbiL in complex with S-adenosylhomocysteine, a methyltransferase involved in anaerobic vitamin B12 biosynthesis
ComponentsPrecorrin-2 C20-methyltransferase
KeywordsTRANSFERASE / precorrin-2 / cobalt-factor II / tetrapyrrole / S-adenosylmethionine
Function / homology
Function and homology information


precorrin-2 C20-methyltransferase / precorrin-2 C20-methyltransferase activity / cobalamin biosynthetic process / methylation
Similarity search - Function
Precorrin-2 C(20)-methyltransferase / Uroporphyrin-III C-methyltransferase signature 1. / Uroporphiryn-III C-methyltransferase, conserved site / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases ...Precorrin-2 C(20)-methyltransferase / Uroporphyrin-III C-methyltransferase signature 1. / Uroporphiryn-III C-methyltransferase, conserved site / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Precorrin-2 C20-methyltransferase
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWada, K. / Fukuyama, K.
CitationJournal: Febs J. / Year: 2007
Title: Crystal structures of CbiL, a methyltransferase involved in anaerobic vitamin B biosynthesis, and CbiL in complex with S-adenosylhomocysteine--implications for the reaction mechanism.
Authors: Wada, K. / Harada, J. / Yaeda, Y. / Tamiaki, H. / Oh-Oka, H. / Fukuyama, K.
History
DepositionOct 10, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 / 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: Precorrin-2 C20-methyltransferase
B: Precorrin-2 C20-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9604
Polymers55,1912
Non-polymers7692
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-22 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.822, 87.822, 123.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-364-

HOH

DetailsThe biological assembly is a homodimer in the asymmetric unit.

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Components

#1: Protein Precorrin-2 C20-methyltransferase


Mass: 27595.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: cbiL / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8KFD9, precorrin-2 C20-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350, 0.2M ammonium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 33275 / Num. obs: 33275 / % possible obs: 99.6 % / Redundancy: 11.2 % / Rsym value: 0.071 / Net I/σ(I): 11
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rsym value: 0.327 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E0K

2e0k


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.182 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26598 1679 5.1 %RANDOM
Rwork0.22263 ---
obs0.2248 31513 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 52 184 3688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9782.0124839
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3035463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47622.846123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47315581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6871527
X-RAY DIFFRACTIONr_chiral_restr0.1520.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.21775
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22431
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9841.52410
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49923734
X-RAY DIFFRACTIONr_scbond_it2.12531326
X-RAY DIFFRACTIONr_scangle_it3.1264.51105
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 111 -
Rwork0.242 2197 -
obs--96.25 %
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)
13.8769-1.2672.42514.9121-0.45493.10810.48460.0386-0.59850.0348-0.06310.35040.56210.0783-0.42150.1006-0.0036-0.0989-0.1478-0.02790.022429.6421.8929.437
26.2940.2870.54688.64142.19024.68680.3722-0.3869-0.83451.30630.1368-0.74641.27560.3422-0.5090.35240.0552-0.2283-0.06430.05110.068738.2741.27337.602
35.2051-0.09291.23373.28541.42572.66860.0237-0.94220.33480.4912-0.44551.09340.2206-0.77220.4218-0.0498-0.09820.21260.1649-0.16690.288616.89920.11941.363
49.5466-3.2319-0.621613.5863-2.74070.73770.44320.0249-0.1111-0.8226-0.02752.51160.46940.3618-0.41570.77740.0919-0.25460.2007-0.2350.392910.3618.58538.274
54.603-1.79152.50556.6459-0.80693.4457-0.25950.90650.759-1.2108-0.1644-0.1061-0.49190.46190.42390.2823-0.0538-0.09030.06090.1991-0.004929.96527.88915.966
63.4791-0.20471.07115.541-1.05235.3612-0.02170.46911.0615-0.953-0.01071.2832-0.6079-0.62930.03240.18060.1304-0.28840.04490.17340.441717.80130.71118.213
73.80010.61121.19913.630.93132.7951-0.0799-0.34590.69470.2046-0.1105-0.0191-0.32130.13980.19040.0068-0.0635-0.007-0.0511-0.04960.082238.20228.79439.692
82.8924-0.24560.60153.5798-1.55294.15530.1221-0.23230.38180.1237-0.1258-0.2444-0.0780.39450.0037-0.0904-0.0857-0.0467-0.0492-0.0120.012243.90225.73938.884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 605 - 60
2X-RAY DIFFRACTION2AA61 - 12761 - 127
3X-RAY DIFFRACTION3AA128 - 215128 - 215
4X-RAY DIFFRACTION4AA216 - 242216 - 242
5X-RAY DIFFRACTION5BB6 - 786 - 78
6X-RAY DIFFRACTION6BB79 - 12979 - 129
7X-RAY DIFFRACTION7BB130 - 219130 - 219
8X-RAY DIFFRACTION8BB220 - 245220 - 245

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