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- PDB-2e0k: Crystal structure of CbiL, a methyltransferase involved in anaero... -

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Basic information

Entry
Database: PDB / ID: 2e0k
TitleCrystal structure of CbiL, 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
Precorrin-2 C20-methyltransferase
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)55,1912
Polymers55,1912
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-24 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.214, 88.214, 123.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
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: 2.1→50 Å / Num. all: 29174 / Num. obs: 29174 / % possible obs: 99.9 % / Redundancy: 15.5 % / Rsym value: 0.053 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 12.9 % / Rsym value: 0.266 / % possible all: 99.7

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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 2CBF

2cbf


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / SU B: 10.145 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27317 1478 5.1 %RANDOM
Rwork0.21839 ---
obs0.22116 27638 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.788 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 0 151 3754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223662
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.9894966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82722.889135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0415607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4251530
X-RAY DIFFRACTIONr_chiral_restr0.1310.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022722
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.21840
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22527
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2271.52480
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95523868
X-RAY DIFFRACTIONr_scbond_it2.76531326
X-RAY DIFFRACTIONr_scangle_it4.1414.51098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 112 -
Rwork0.196 1968 -
obs--98.62 %
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)
11.6674-0.48061.14683.0625-0.40792.23780.31780.0534-0.24380.0573-0.05460.20620.33090.1094-0.26320.1319-0.0202-0.074-0.0121-0.01940.016931.2650.48830.713
238.09659.80215.795626.34850.895716.36150.7143-5.06261.43332.3587-0.3573.24040.5627-1.1997-0.35720.46020.0009-0.0120.45310.0030.459734.938-2.38748.254
31.3312-0.52830.7392.72750.85561.39590.2227-0.0874-0.02530.3749-0.0213-0.00330.25760.093-0.20140.1207-0.0136-0.02170.03620.0113-0.017434.66810.36635.541
43.23510.8393-0.04171.04210.48364.67420.0932-0.34260.030.2885-0.0970.35040.1006-0.69320.0038-0.046-0.03340.15070.0959-0.04510.150412.95119.24842.112
52.6617-1.02580.98143.6654-0.34850.62810.02520.30530.1765-0.6966-0.22040.0134-0.01840.17030.19520.22-0.0078-0.04530.07820.0536-0.060429.38125.04115.43
63.6667-0.2654-0.13117.4002-2.84162.3728-0.11170.52320.6971-0.47710.10870.5121-0.1387-0.09960.0030.10970.0304-0.19040.04220.1765-0.031924.58733.30814.145
71.64920.16890.8051.3106-0.16221.11820.012-0.01120.2116-0.0158-0.05960.3442-0.13420.03590.04770.08850.00510.00490.0012-0.01360.084125.76126.45230.521
82.70990.916-0.52333.0079-0.62461.33140.0335-0.14020.38060.2186-0.0234-0.0206-0.13260.1291-0.01010.0606-0.0526-0.00850.0235-0.02650.016142.30229.79439.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 711 - 71
2X-RAY DIFFRACTION2AA72 - 8772 - 87
3X-RAY DIFFRACTION3AA88 - 15288 - 152
4X-RAY DIFFRACTION4AA153 - 245153 - 245
5X-RAY DIFFRACTION5BB2 - 552 - 55
6X-RAY DIFFRACTION6BB56 - 9856 - 98
7X-RAY DIFFRACTION7BB99 - 16399 - 163
8X-RAY DIFFRACTION8BB164 - 245164 - 245

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