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- PDB-1l3i: MT0146, THE PRECORRIN-6Y METHYLTRANSFERASE (CBIT) HOMOLOG FROM M.... -

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Basic information

Entry
Database: PDB / ID: 1l3i
TitleMT0146, THE PRECORRIN-6Y METHYLTRANSFERASE (CBIT) HOMOLOG FROM M. THERMOAUTOTROPHICUM, ADOHCY BINARY COMPLEX
ComponentsPrecorrin-6y methyltransferase/putative decarboxylase
KeywordsTRANSFERASE / LYASE / STRUCTURAL GENOMICS / BETA BARREL / ROSSMANN FOLD / TETRAMER / METHYLTRANSFERASE / DECARBOXYLASE / STRUCTURE-BASED FUNCTION ASSIGNMENT
Function / homology
Function and homology information


cobalt-precorrin-6B (C15)-methyltransferase [decarboxylating] / cobalt-precorrin-6B C5-methyltransferase activity / anaerobic cobalamin biosynthetic process / protein methyltransferase activity / methylation
Similarity search - Function
Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) CbiT / Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit / : / Methyltransferase domain / 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
S-ADENOSYL-L-HOMOCYSTEINE / Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKeller, J.P. / Smith, P.M. / Benach, J. / Christendat, D. / deTitta, G. / Hunt, J.F.
CitationJournal: Structure / Year: 2002
Title: The Crystal Structure of Mt0146/CbiT Suggests that the Putative Precorrin-8W Decarboxylase is a Methyltransferase
Authors: Keller, J.P. / Smith, P.M. / Benach, J. / Christendat, D. / deTitta, G. / Hunt, J.F.
History
DepositionFeb 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Precorrin-6y methyltransferase/putative decarboxylase
B: Precorrin-6y methyltransferase/putative decarboxylase
C: Precorrin-6y methyltransferase/putative decarboxylase
D: Precorrin-6y methyltransferase/putative decarboxylase
E: Precorrin-6y methyltransferase/putative decarboxylase
F: Precorrin-6y methyltransferase/putative decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,97912
Polymers126,6736
Non-polymers2,3066
Water13,097727
1
A: Precorrin-6y methyltransferase/putative decarboxylase
B: Precorrin-6y methyltransferase/putative decarboxylase
C: Precorrin-6y methyltransferase/putative decarboxylase
D: Precorrin-6y methyltransferase/putative decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9868
Polymers84,4494
Non-polymers1,5384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-61 kcal/mol
Surface area29940 Å2
MethodPISA
2
E: Precorrin-6y methyltransferase/putative decarboxylase
F: Precorrin-6y methyltransferase/putative decarboxylase
hetero molecules

E: Precorrin-6y methyltransferase/putative decarboxylase
F: Precorrin-6y methyltransferase/putative decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9868
Polymers84,4494
Non-polymers1,5384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
3
A: Precorrin-6y methyltransferase/putative decarboxylase
B: Precorrin-6y methyltransferase/putative decarboxylase
C: Precorrin-6y methyltransferase/putative decarboxylase
D: Precorrin-6y methyltransferase/putative decarboxylase
E: Precorrin-6y methyltransferase/putative decarboxylase
F: Precorrin-6y methyltransferase/putative decarboxylase
hetero molecules

A: Precorrin-6y methyltransferase/putative decarboxylase
B: Precorrin-6y methyltransferase/putative decarboxylase
C: Precorrin-6y methyltransferase/putative decarboxylase
D: Precorrin-6y methyltransferase/putative decarboxylase
E: Precorrin-6y methyltransferase/putative decarboxylase
F: Precorrin-6y methyltransferase/putative decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,95924
Polymers253,34612
Non-polymers4,61312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area35400 Å2
ΔGint-196 kcal/mol
Surface area83220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.1, 59.4, 165.9
Angle α, β, γ (deg.)90, 109.9, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Precorrin-6y methyltransferase/putative decarboxylase / MT0146 / cbiT / MTH146


Mass: 21112.131 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: Mth146 / Plasmid: B834 Codon+ / Production host: Escherichia coli (E. coli) / References: UniProt: O26249
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, MgCl, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15-10 mg/mlprotein1drop
210 %(w/v)PEG80001drop
3100 mM1dropMgCl2
45 mMTris-Cl1droppH7.5
516-22 %PEG80001reservoir
6200 mM1reservoirMgCl2
710 mMTris-Cl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2000
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 91883 / % possible obs: 97.8 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.37 %
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 97.7 % / Redundancy: 3.34 % / Rmerge(I) obs: 0.14
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 1.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F38

1f38


Resolution: 1.95→26.17 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4012 4.4 %RANDOM
Rwork0.212 ---
obs-91883 --
Refinement stepCycle: LAST / Resolution: 1.95→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8352 0 156 727 9235
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.2577 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS

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