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- PDB-1x19: Crystal structure of BchU involved in bacteriochlorophyll c biosy... -

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Basic information

Entry
Database: PDB / ID: 1x19
TitleCrystal structure of BchU involved in bacteriochlorophyll c biosynthesis
ComponentsCrtF-related protein
KeywordsTRANSFERASE / METHYLTRANSFERASE / BACTERIOCHLLOCHLOROPHYLL / BchU / SAM / SAH / S-ADENOSYLMETHYONINE / S-ADENOSYLHOMOCYSTEINE / ADO-MET / ADO-HCY
Function / homology
Function and homology information


bacteriochlorophyllide d C-20 methyltransferase / light-dependent bacteriochlorophyll biosynthetic process / light-independent bacteriochlorophyll biosynthetic process / O-methyltransferase activity / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
C-20 methyltransferase CrtF-related / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...C-20 methyltransferase CrtF-related / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Bacteriochlorophyllide d C-20 methyltransferase
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.27 Å
AuthorsYamaguchi, H. / Wada, K. / Fukuyama, K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of BchU, a Methyltransferase Involved in Bacteriochlorophyll c Biosynthesis, and its Complex with S-adenosylhomocysteine: Implications for Reaction Mechanism.
Authors: Wada, K. / Yamaguchi, H. / Harada, J. / Niimi, K. / Osumi, S. / Saga, Y. / Oh-Oka, H. / Tamiaki, H. / Fukuyama, K.
History
DepositionApr 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CrtF-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3762
Polymers40,2801
Non-polymers961
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CrtF-related protein
hetero molecules

A: CrtF-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7534
Polymers80,5602
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area8430 Å2
ΔGint-89 kcal/mol
Surface area29550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.543, 81.543, 250.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-4509-

HOH

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Components

#1: Protein CrtF-related protein / methyltransferase


Mass: 40280.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8KGE0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS, 1.5M ammonium sulfate, 12% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
3931
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B111
SYNCHROTRONSPring-8 BL38B121
SYNCHROTRONSPring-8 BL41XU30.9794, 0.9796, 0.9843
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 25, 2004
ADSC QUANTUM 42CCDMay 25, 2004
ADSC QUANTUM 3153CCDMay 29, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
30.97961
40.98431
ReflectionResolution: 2.27→50 Å / Num. obs: 23709 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 11.3 % / Rsym value: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 10.9 % / Rsym value: 0.22 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.27→38.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 435211.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2187 9.6 %RANDOM
Rwork0.206 ---
all0.211 ---
obs0.206 22822 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1536 Å2 / ksol: 0.366535 e/Å3
Displacement parametersBiso mean: 47.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.98 Å27.59 Å20 Å2
2--8.98 Å20 Å2
3----17.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.27→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 5 128 2883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.44
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.931.5
X-RAY DIFFRACTIONc_mcangle_it5.072
X-RAY DIFFRACTIONc_scbond_it6.012
X-RAY DIFFRACTIONc_scangle_it7.582.5
LS refinement shellResolution: 2.27→2.41 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 249 7 %
Rwork0.243 3325 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4_xplor_par.txtso4_xplor_top.txt

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