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- PDB-1jdx: CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE ... -

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Basic information

Entry
Database: PDB / ID: 1jdx
TitleCRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH L-NORVALINE
ComponentsPROTEIN (L-ARGININE:GLYCINE AMIDINOTRANSFERASE)
KeywordsTRANSFERASE / CREATINE BIOSYNTHESIS / CATALYTIC TRIAD / REACTION MECHANISM / NOVEL FOLD / FIVEFOLD PSEUDOSYMMETRY
Function / homologyPortal protein / Phage portal protein, SPP1 Gp6-like / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta / NORVALINE / Portal protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsFritsche, E. / Humm, A. / Huber, R.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study.
Authors: Fritsche, E. / Humm, A. / Huber, R.
History
DepositionOct 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (L-ARGININE:GLYCINE AMIDINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4592
Polymers44,3411
Non-polymers1171
Water2,396133
1
A: PROTEIN (L-ARGININE:GLYCINE AMIDINOTRANSFERASE)
hetero molecules

A: PROTEIN (L-ARGININE:GLYCINE AMIDINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9174
Polymers88,6832
Non-polymers2342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_465x-1/2,-y+3/2,-z+1/41
Unit cell
Length a, b, c (Å)83.800, 83.800, 199.600
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 PROTEIN (L-ARGININE:GLYCINE AMIDINOTRANSFERASE) / TRANSAMIDINASE / AT38


Mass: 44341.488 Da / Num. of mol.: 1 / Fragment: RESIDUES 38 - 423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL(21)DE3PLYSS / Cellular location: CYTOSOLIC / Gene: AT38H / Organ: KIDNEY / Organelle: MITOCHONDRIA / Plasmid: PRSETAT38H / Gene (production host): AT38H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P50440, EC: 2.1.4.1
#2: Chemical ChemComp-NVA / NORVALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.83 Å3/Da / Density % sol: 68 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop was made of a 7 micro litter protein solution and 14 micro litter of a reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
230 mMHEPES-NaOH1drop
30.5 mMEDTA1drop
40.5 mMGSH1drop
53 %(w/v)PEG60001reservoir
640 mMHEPES-NaOH1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 20930 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.115
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 27837 / Num. measured all: 108578 / Rmerge(I) obs: 98.6 / Rmerge F obs: 0.095
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.353

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.4→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.177 --
obs0.177 27030 98.6 %
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 8 133 3079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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