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- PDB-3jdw: CRYSTAL STRUCTURE AND MECHANISM OF L-ARGININE: GLYCINE AMIDINOTRA... -

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Basic information

Entry
Database: PDB / ID: 3jdw
TitleCRYSTAL STRUCTURE AND MECHANISM OF L-ARGININE: GLYCINE AMIDINOTRANSFERASE: A MITOCHONDRIAL ENZYME INVOLVED IN CREATINE BIOSYNTHESIS
ComponentsL-ARGININE\:GLYCINE AMIDINOTRANSFERASE
KeywordsTRANSFERASE / CREATINE BIOSYNTHESIS / CATALYTIC TRIAD / REACTION MECHANISM / NOVEL FOLD / FIVEFOLD PSEUDOSYMMETRY
Function / homology
Function and homology information


glycine amidinotransferase / glycine amidinotransferase activity / amidinotransferase activity / creatine metabolic process / Creatine metabolism / creatine biosynthetic process / muscle atrophy / mitochondrial intermembrane space / positive regulation of cold-induced thermogenesis / mitochondrial inner membrane ...glycine amidinotransferase / glycine amidinotransferase activity / amidinotransferase activity / creatine metabolic process / Creatine metabolism / creatine biosynthetic process / muscle atrophy / mitochondrial intermembrane space / positive regulation of cold-induced thermogenesis / mitochondrial inner membrane / learning or memory / mitochondrion / extracellular exosome
Similarity search - Function
Glycine/inosamine-phosphate amidinotransferase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
L-ornithine / Glycine amidinotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH PDB ENTRY 1JDW / Resolution: 2.4 Å
AuthorsHumm, A. / Fritsche, E. / Steinbacher, S. / Huber, R.
Citation
Journal: EMBO J. / Year: 1997
Title: Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.
Authors: Humm, A. / Fritsche, E. / Steinbacher, S. / Huber, R.
#1: Journal: Biol.Chem.Hoppe-Seyler / Year: 1997
Title: Structure and Reaction Mechanism of L-Arginine:Glycine Amidinotransferase
Authors: Humm, A. / Fritsche, E. / Steinbacher, S.
#2: Journal: Eur.J.Biochem. / Year: 1997
Title: Substrate Binding and Catalysis by L-Arginine:Glycine Amidinotransferase--A Mutagenesis and Crystallographic Study
Authors: Fritsche, E. / Humm, A. / Huber, R.
#3: Journal: Biochem.J. / Year: 1997
Title: Recombinant Expression and Isolation of Human L-Arginine:Glycine Amidinotransferase and Identification of its Active-Site Cysteine Residue
Authors: Humm, A. / Fritsche, E. / Mann, K. / Gohl, M. / Huber, R.
#4: Journal: J.Mol.Biol. / Year: 1997
Title: Bioincorporation of Telluromethionine Into Proteins: A Promising New Approach for X-Ray Structure Analysis of Proteins
Authors: Budisa, N. / Karnbrock, W. / Steinbacher, S. / Humm, A. / Prade, L. / Neuefeind, T. / Moroder, L. / Huber, R.
History
DepositionJan 24, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _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: L-ARGININE\:GLYCINE AMIDINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6542
Polymers48,5211
Non-polymers1321
Water3,477193
1
A: L-ARGININE\:GLYCINE AMIDINOTRANSFERASE
hetero molecules

A: L-ARGININE\:GLYCINE AMIDINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3074
Polymers97,0432
Non-polymers2642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)83.760, 83.760, 199.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein L-ARGININE\:GLYCINE AMIDINOTRANSFERASE / TRANSAMIDINASE / AT38


Mass: 48521.367 Da / Num. of mol.: 1 / Fragment: RESIDUES 64 - 423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: WITHOUT SIGNAL SEQUENCE (1-37) BUT WITH N-TERMINAL ATTACHED 6-HISTIDINE-TAG (14 RESIDUES)
Cell line: BL21
Cellular location: INTERMEMBRANE SPACE OF MITOCHONDRIA AND CYTOPLASM
Gene: AT38H / Organ: KIDNEY / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PRSETAT38H / Cellular location (production host): CYTOSOLIC / Gene (production host): AT38H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P50440, glycine amidinotransferase
#2: Chemical ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.8 Å3/Da / Density % sol: 65 %
Crystal growpH: 7
Details: 1 PART OF AT38H (13-16 MG/ML) 2 PARTS OF PRECIPITANT (3% PEG 6000, 40 MM HEPES, 1MM GLUTATHIONE, PH7.0), SEVERAL DAYS AT ROOM TEMPERATURE, MACRO SEEDING.
Temp details: room temp
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-15 mg/mlprotein1drop
23 %PEG60001reservoir
340 mMHEPES1reservoir
42 mMbeta-ME1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→8 Å / Num. obs: 25838 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 3.78 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.4→2.43 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.287 / % possible all: 51.9
Reflection shell
*PLUS
% possible obs: 51.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMV. 5.23data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1JDW
Starting model: PDB ENTRY 1JDW

1jdw


Resolution: 2.4→8 Å / Cross valid method: FREE R / σ(F): 0
Details: RESIDUES 38 - 63 ARE NOT VISIBLE IN THE ELECTRON DENSITY
RfactorNum. reflection% reflection
Rwork0.181 --
obs0.181 25838 93.1 %
Displacement parametersBiso mean: 27.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 9 193 3140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.11
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.43 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rwork0.302 458 -
obs--51.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.11
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.42

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