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- PDB-3njr: Crystal structure of C-terminal domain of precorrin-6Y C5,15-meth... -

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Basic information

Entry
Database: PDB / ID: 3njr
TitleCrystal structure of C-terminal domain of precorrin-6Y C5,15-methyltransferase from Rhodobacter capsulatus
ComponentsPrecorrin-6y methylase
KeywordsTRANSFERASE / methyltransferase / decarboxylase
Function / homology
Function and homology information


precorrin-6B C5,15-methyltransferase (decarboxylating) / precorrin-6Y C5,15-methyltransferase (decarboxylating) activity / cobalamin biosynthetic process / protein methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
Cobalamin (vitamin B12) biosynthesis CobL/Precorrin-6Y C(5,15)-methyltransferase / Precorrin-6Y methyltransferase / Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit / : / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Cobalamin (vitamin B12) biosynthesis CobL/Precorrin-6Y C(5,15)-methyltransferase / Precorrin-6Y methyltransferase / Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit / : / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 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 / Precorrin-6Y C5,15-methyltransferase (Decarboxylating) / Precorrin-6y methylase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSeyedarabi, A. / Pickersgill, R.W.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.
Authors: Deery, E. / Schroeder, S. / Lawrence, A.D. / Taylor, S.L. / Seyedarabi, A. / Waterman, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. / Pickersgill, R.W. / Warren, M.J.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Sep 6, 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

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Assembly

Deposited unit
A: Precorrin-6y methylase
B: Precorrin-6y methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1817
Polymers44,0342
Non-polymers1,1475
Water55831
1
A: Precorrin-6y methylase
B: Precorrin-6y methylase
hetero molecules

A: Precorrin-6y methylase
B: Precorrin-6y methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,36214
Polymers88,0684
Non-polymers2,29410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area11980 Å2
ΔGint-43 kcal/mol
Surface area27660 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-11 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.354, 44.799, 84.110
Angle α, β, γ (deg.)90.00, 119.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Precorrin-6y methylase


Mass: 22016.939 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 214-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Strain: SB1003 / Gene: cobL / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLySs
References: UniProt: O68099, UniProt: D5AV04*PLUS, precorrin-6B C5,15-methyltransferase (decarboxylating)
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M tri-sodium citrate dihydrate pH 5.6, 20% isopropanol and 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.011 Å / Relative weight: 1
ReflectionResolution: 2.7→72.93 Å / Num. all: 10412 / Num. obs: 10402 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.214 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HM2

3hm2


Resolution: 2.7→40.54 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.677 / SU ML: 0.288 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26483 499 4.8 %RANDOM
Rwork0.18493 ---
obs0.18868 9897 99.88 %-
all-9909 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 77 31 2898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212928
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9883973
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55422.295122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.21415458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2611534
X-RAY DIFFRACTIONr_chiral_restr0.0960.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212224
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6411.51830
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23322906
X-RAY DIFFRACTIONr_scbond_it1.80431098
X-RAY DIFFRACTIONr_scangle_it3.14.51067
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 44 -
Rwork0.241 737 -
obs--99.87 %

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