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- PDB-1x1c: Crystal structure of BchU complexed with S-adenosyl-L-homocystein... -

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Basic information

Entry
Database: PDB / ID: 1x1c
TitleCrystal structure of BchU complexed with S-adenosyl-L-homocysteine and Zn2+
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
S-ADENOSYL-L-HOMOCYSTEINE / Bacteriochlorophyllide d C-20 methyltransferase
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 3, 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 1.3Oct 25, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: CrtF-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1809
Polymers40,2801
Non-polymers9008
Water36020
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)82,36018
Polymers80,5602
Non-polymers1,79916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area9980 Å2
ΔGint-391 kcal/mol
Surface area26660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.615, 81.615, 250.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 28 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
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

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1.25 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 12397 / % possible obs: 100 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 172.2 Å2 / Rsym value: 0.064 / Net I/σ(I): 13.2
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 20.9 % / Rsym value: 0.322 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X1B

1x1b


Resolution: 2.85→41.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 290003.9 / 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
Rfree0.288 1199 10.3 %RANDOM
Rwork0.23 ---
all0.236 ---
obs0.23 11610 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.813 Å2 / ksol: 0.384645 e/Å3
Displacement parametersBiso mean: 71 Å2
Baniso -1Baniso -2Baniso -3
1-18.99 Å217.59 Å20 Å2
2--18.99 Å20 Å2
3----37.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.85→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 42 20 2717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.151.5
X-RAY DIFFRACTIONc_mcangle_it7.282
X-RAY DIFFRACTIONc_scbond_it8.042
X-RAY DIFFRACTIONc_scangle_it10.392.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 171 9.8 %
Rwork0.317 1580 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4so4_xplor_par.txt&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5sah_xplor_par.txt&_1_TOPOLOGY_INFILE_5

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