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- PDB-1v9a: Crystal structure of Uroporphyrin-III C-methyl transferase from T... -

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Basic information

Entry
Database: PDB / ID: 1v9a
TitleCrystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus complexed with S-adenyl homocysteine
ComponentsUroporphyrin-III C-methyltransferaseUroporphyrinogen-III C-methyltransferase
KeywordsTRANSFERASE / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


uroporphyrinogen-III C-methyltransferase / uroporphyrin-III C-methyltransferase activity / siroheme biosynthetic process / methylation
Similarity search - Function
Uroporphyrin-III C-methyltransferase / Uroporphyrin-III C-methyltransferase signature 2. / 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 ...Uroporphyrin-III C-methyltransferase / Uroporphyrin-III C-methyltransferase signature 2. / 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
CITRATE ANION / S-ADENOSYL-L-HOMOCYSTEINE / uroporphyrinogen-III C-methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRehse, P.H. / Kitao, T. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus.
Authors: Rehse, P.H. / Kitao, T. / Tahirov, T.H.
History
DepositionJan 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uroporphyrin-III C-methyltransferase
B: Uroporphyrin-III C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4346
Polymers52,2872
Non-polymers1,1474
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-39 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.982, 63.810, 132.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe two chains in the asymmetric unit constitute the biological assembly.

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Components

#1: Protein Uroporphyrin-III C-methyltransferase / Uroporphyrinogen-III C-methyltransferase / hypothetical protein TTHA0667


Mass: 26143.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q5SKH6, uroporphyrinogen-III C-methyltransferase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.42 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: Citrate, PEG 20000, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 8, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→41.5 Å / Num. all: 38702 / Num. obs: 38702 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.97 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.1
Reflection shellResolution: 1.93→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.03 / Num. unique all: 3792 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1CBF

1cbf


Resolution: 2→41.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1031703.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1678 5 %RANDOM
Rwork0.215 ---
obs0.215 33592 95.7 %-
all-33592 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.3012 Å2 / ksol: 0.345573 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.98 Å20 Å20 Å2
2--2.4 Å20 Å2
3----6.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 78 209 3737
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it3.391.5
X-RAY DIFFRACTIONc_mcangle_it4.442
X-RAY DIFFRACTIONc_scbond_it4.62
X-RAY DIFFRACTIONc_scangle_it6.192.5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 162 5.6 %
Rwork0.287 4968 -
obs-3149 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SAH.PARAMSAH.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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