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- PDB-3orh: Human guanidinoacetate N-methyltransferase with SAH -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3orh
TitleHuman guanidinoacetate N-methyltransferase with SAH
ComponentsGuanidinoacetate N-methyltransferase
KeywordsTRANSFERASE / GUANIDINOACETATE N-METHYLTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine metabolic process / Creatine metabolism / creatine biosynthetic process / Transcriptional Regulation by MECP2 / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / muscle contraction / methyltransferase activity ...guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine metabolic process / Creatine metabolism / creatine biosynthetic process / Transcriptional Regulation by MECP2 / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / muscle contraction / methyltransferase activity / animal organ morphogenesis / methylation / spermatogenesis / nucleus / cytosol / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsDong, A. / Wu, H. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of human guanidinoacetate N-methyltransferase with SAH
Authors: Wu, H. / Dong, A. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionSep 7, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionSep 15, 2010ID: 1ZX0
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Guanidinoacetate N-methyltransferase
B: Guanidinoacetate N-methyltransferase
C: Guanidinoacetate N-methyltransferase
D: Guanidinoacetate N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9268
Polymers105,3884
Non-polymers1,5384
Water17,673981
1
A: Guanidinoacetate N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7322
Polymers26,3471
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Guanidinoacetate N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7322
Polymers26,3471
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Guanidinoacetate N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7322
Polymers26,3471
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Guanidinoacetate N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7322
Polymers26,3471
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)200.327, 200.327, 52.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein
Guanidinoacetate N-methyltransferase /


Mass: 26347.123 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAMT / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14353, guanidinoacetate N-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


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


Mass: 18.015 Da / Num. of mol.: 981 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 6.5
Details: 21% PEG3350, 0.1M CACL2, 0.1M TRIS, 1MM GUANIDINE HCL, pH 6.5, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9766 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 9, 2005 / Details: SI(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.86→37.2 Å / Num. all: 97258 / Num. obs: 97258 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.7 / Rsym value: 0.7 / Net I/σ(I): 21.2
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3582 / % possible all: 74

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XCL

1xcl


Resolution: 1.86→37.2 Å / Cor.coef. Fo:Fc: 0.9154 / Cor.coef. Fo:Fc free: 0.8976 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 973 1 %RANDOM
Rwork0.2086 ---
all0.2088 ---
obs-97237 --
Displacement parametersBiso max: 207.74 Å2 / Biso mean: 24.6722 Å2 / Biso min: 8.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.7103 Å20 Å20 Å2
2---0.7103 Å20 Å2
3---1.4205 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 1.86→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7162 0 104 981 8247
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d24662
X-RAY DIFFRACTIONt_trig_c_planes1532
X-RAY DIFFRACTIONt_gen_planes10915
X-RAY DIFFRACTIONt_it751520
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion9555
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact93454
X-RAY DIFFRACTIONt_bond_d751520.01
X-RAY DIFFRACTIONt_angle_deg1026020.97
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion16.29
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2145 52 0.94 %
Rwork0.2317 5480 -
all0.2315 5532 -

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