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- PDB-4jdw: CRYSTAL STRUCTURE AND MECHANISM OF L-ARGININE: GLYCINE AMIDINOTRA... -

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Basic information

Entry
Database: PDB / ID: 4jdw
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
ARGININE / Glycine amidinotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH PDB ENTRY 1JDW / Resolution: 2.5 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: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-ARGININE\:GLYCINE AMIDINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6652
Polymers48,4891
Non-polymers1751
Water3,513195
1
A: L-ARGININE\:GLYCINE AMIDINOTRANSFERASE
hetero molecules

A: L-ARGININE\:GLYCINE AMIDINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3294
Polymers96,9792
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)83.780, 83.780, 199.450
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: 48489.305 Da / Num. of mol.: 1 / Fragment: RESIDUES 64 - 423
Mutation: WITHOUT SIGNAL SEQUENCE (1-37) BUT WITH N-TERMINAL ATTACHED 6-HISTIDINE-TAG (14 RESIDUES), C407A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21
Cellular location: INTERMEMBRANE SPACE OF MITOCHONDRIA AND CYTOPLASM
Gene: AT38H / Organ: KIDNEY / Organelle: MITOCHONDRIA / 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-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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. L-ARGININE WAS SOAKED INTO CRYSTAL ...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. L-ARGININE WAS SOAKED INTO CRYSTAL AND IS BOUND TO ACTIVE SITE.
Temp details: room temp
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.3-5 mg/mlprotein1drop
22 %PEG60001drop
327 mMHEPES1drop
41.3 mMbeta-ME1drop
53 %PEG60001reservoir
640 mMHEPES1reservoir
72 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: Dec 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→8 Å / Num. obs: 22282 / % possible obs: 87.2 % / Observed criterion σ(I): 0 / Redundancy: 3.76 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.5→2.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.261 / % possible all: 81.3

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Processing

Software
NameVersionClassification
MOSFLM5.23data reduction
ROTAVATA/AGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1JDW
Starting model: PDB ENTRY 1JDW

1jdw


Resolution: 2.5→8 Å / Cross valid method: FREE R / σ(F): 0
Details: RESIDUES 38 - 63 ARE NOT VISIBLE IN THE ELECTRON DENSITY
RfactorNum. reflection% reflection
Rwork0.183 --
obs0.183 21405 87.2 %
Displacement parametersBiso mean: 23.58 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 11 194 3145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.684
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.54
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: 2.5→2.53 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rwork0.261 656 -
obs--81.3 %
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_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.54

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