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- PDB-1p1c: Guanidinoacetate Methyltransferase with Gd ion -

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Basic information

Entry
Database: PDB / ID: 1p1c
TitleGuanidinoacetate Methyltransferase with Gd ion
ComponentsGuanidinoacetate N-methyltransferase
KeywordsTRANSFERASE / Guanidinoacetate methyltransferase / Methyltransferase / Gd ion / S-adenosylhomocysteine
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
GADOLINIUM ION / S-ADENOSYL-L-HOMOCYSTEINE / Guanidinoacetate N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKomoto, J. / Takusagawa, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Monoclinic guanidinoacetate methyltransferase and gadolinium ion-binding characteristics.
Authors: Komoto, J. / Takata, Y. / Yamada, T. / Konishi, K. / Ogawa, H. / Gomi, T. / Fujioka, M. / Takusagawa, F.
History
DepositionApr 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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.ptnr2_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The authors of this entry state that the authors of the original sequence paper (PNAS 85, ...SEQUENCE The authors of this entry state that the authors of the original sequence paper (PNAS 85, 694 (1988)) stated that Glu-119 was wrong and the correct amino acid residue is Val.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,1565
Polymers45,2302
Non-polymers9263
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-16 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.22, 54.22, 156.27
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Guanidinoacetate N-methyltransferase


Mass: 22615.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GAMT / 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: Chemical ChemComp-GD3 / GADOLINIUM ION


Mass: 157.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Gd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
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: Jan 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→20 Å / Num. all: 16012 / Num. obs: 16012 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.054
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.098 / % possible all: 87
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 54.5 Å / Num. obs: 14284 / Num. measured all: 110383
Reflection shell
*PLUS
% possible obs: 81.3 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR98.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 1341 RANDOM
Rwork0.193 --
all0.211 14012 -
obs0.194 13620 -
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 53 196 3345
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
Refinement
*PLUS
Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.384 / Rfactor Rwork: 0.251

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