[English] 日本語
Yorodumi
- PDB-2e0k: Crystal structure of CbiL, a methyltransferase involved in anaero... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more