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- PDB-1cbf: THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PR... -

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Basic information

Entry
Database: PDB / ID: 1cbf
TitleTHE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF
ComponentsCOBALT-PRECORRIN-4 TRANSMETHYLASE
KeywordsMETHYLTRANSFERASE / PRECORRIN-4 METHYLTRANSFERASE / METHYLASE / COBALAMIN BIOSYNTHESIS
Function / homology
Function and homology information


cobalt-precorrin-4 methyltransferase / precorrin-4 C11-methyltransferase activity / cobalamin biosynthetic process / methylation
Similarity search - Function
Cobalamin (vitamin B12) biosynthesis CobM/CbiF, precorrin-4 C11-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 ...Cobalamin (vitamin B12) biosynthesis CobM/CbiF, precorrin-4 C11-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
PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Cobalt-precorrin-4 C(11)-methyltransferase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsSchubert, H.L. / Raux, E. / Woodcock, S.C. / Wilson, K.S. / Warren, M.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase.
Authors: Schubert, H.L. / Wilson, K.S. / Raux, E. / Woodcock, S.C. / Warren, M.J.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: Cobalamin (Vitamin B12) Biosynthesis--Cloning, Expression and Crystallisation of the Bacillus Megaterium S-Adenosyl-L-Methionine-Dependent Cobalt-Precorrin-4 Transmethylase Cbif
Authors: Raux, E. / Schubert, H.L. / Woodcock, S.C. / Wilson, K.S. / Warren, M.J.
History
DepositionMay 1, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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: COBALT-PRECORRIN-4 TRANSMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5704
Polymers30,9961
Non-polymers5743
Water2,432135
1
A: COBALT-PRECORRIN-4 TRANSMETHYLASE
hetero molecules

A: COBALT-PRECORRIN-4 TRANSMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1418
Polymers61,9922
Non-polymers1,1496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+4/31
Buried area5240 Å2
ΔGint-57 kcal/mol
Surface area19950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.700, 80.700, 109.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein COBALT-PRECORRIN-4 TRANSMETHYLASE / PRECORRIN-4 METHYLASE / CBIF


Mass: 30996.051 Da / Num. of mol.: 1 / Mutation: HIS-TAGGED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Cell line: BL21 / Gene: CBIF / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS
References: UniProt: O87696, precorrin-4 C11-methyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
pH: 5.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMsodium acetate11
2100 mM11NaCl
316-20 mg/mlprotein12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: PLATINUM COATED TORROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 16587 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.039 / Rsym value: 0.04 / Net I/σ(I): 21.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 10 / Rsym value: 0.115 / % possible all: 100
Reflection
*PLUS
% possible obs: 99.8 %
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→20 Å
Details: FREE R VALUE TEST SET SELECTION WAS RANDOM, BUT FRIEDEL MATES ARE KEPT IN SAME SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 814 5 %RANDOM
Rwork0.195 ---
obs-16587 100 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 36 135 1989
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.204 / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_deg2.3

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