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- PDB-1khh: Crystal Structure of Guanidinoacetate Methyltransferase from Rat ... -

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Basic information

Entry
Database: PDB / ID: 1khh
TitleCrystal Structure of Guanidinoacetate Methyltransferase from Rat Liver: A Template Structure of Protein Arginine Methyltransferase
ComponentsGuanidinoacetate methyltransferase
KeywordsTRANSFERASE / methyltransferase / creatine biosynthesis
Function / homology
Function and homology information


Creatine metabolism / guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine biosynthetic process / embryonic liver development / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / animal organ morphogenesis ...Creatine metabolism / guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine biosynthetic process / embryonic liver development / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / animal organ morphogenesis / spermatogenesis / methylation / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Guanidinoacetate N-methyltransferase / Arginine N-methyltransferase 2-like domain / : / Arginine and arginine-like N-methyltransferase domain profile. / 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 / Guanidinoacetate N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.5 Å
AuthorsTakusagawa, F. / Komoto, J.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of guanidinoacetate methyltransferase from rat liver: a model structure of protein arginine methyltransferase.
Authors: Komoto, J. / Huang, Y. / Takata, Y. / Yamada, T. / Konishi, K. / Ogawa, H. / Gomi, T. / Fujioka, M. / Takusagawa, F.
History
DepositionNov 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE TRUNCATED ENZYME FORMS A HOMODIMER.
Remark 999SEQUENCE According to the authors, the correct amino acid residue is Val (GTG) at position 119. ...SEQUENCE According to the authors, the correct amino acid residue is Val (GTG) at position 119. Therefore, the sequence in the PDB file is the updated and correct one.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanidinoacetate methyltransferase
B: Guanidinoacetate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8854
Polymers45,1162
Non-polymers7692
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-9 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.25, 54.25, 156.56
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43
DetailsThe biological assembly is a monomer. However, the N-terminal truncated enzyme forms a homodimer.

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Components

#1: Protein Guanidinoacetate methyltransferase / Guanidinoacetate N-methyltransferase


Mass: 22557.988 Da / Num. of mol.: 2 / Fragment: N-terminal truncation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: liver / Production host: Escherichia coli (E. coli)
References: UniProt: P10868, guanidinoacetate N-methyltransferase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMMES1reservoirpH6.5
21 mMdithiothreitol1reservoir
32 mMSAH1reservoir
41 mMGAA1reservoir
58 %(w/v)PEG80001reservoir
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 2001 / Details: Confocal optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→34.5 Å / Num. all: 109295 / Num. obs: 109295 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 5 / Num. unique all: 1332 / Rsym value: 0.139 / % possible all: 83.4
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 15472 / % possible obs: 98 % / Num. measured all: 109295

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CCP4model building
X-PLOR3.843refinement
CCP4phasing
RefinementMethod to determine structure: SIR / Resolution: 2.5→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The structure was solved by SIR using Gd-derivative. Residues 38-42 are disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1300 10 %RANDOM
Rwork0.214 ---
all0.228 14000 --
obs0.221 13194 --
Refine analyzeLuzzati coordinate error obs: 0.03 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 52 162 3310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_d1.28
X-RAY DIFFRACTIONx_dihedral_angle_d27
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.5-2.580.3761190.2880.022119483.1
2.58-80.28412000.20.0121200097.8
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection Rfree: 1481 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.28
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.376 / Rfactor Rwork: 0.288 / Rfactor obs: 0.288

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