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- PDB-1aos: HUMAN ARGININOSUCCINATE LYASE -

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Basic information

Entry
Database: PDB / ID: 1aos
TitleHUMAN ARGININOSUCCINATE LYASE
ComponentsARGININOSUCCINATE LYASE
KeywordsLYASE / ARGININE BIOSYNTHESIS / UREA CYCLE
Function / homology
Function and homology information


ammonia assimilation cycle / argininosuccinate lyase / argininosuccinate lyase activity / arginine metabolic process / Urea cycle / arginine biosynthetic process via ornithine / urea cycle / arginine biosynthetic process / post-embryonic development / locomotory behavior ...ammonia assimilation cycle / argininosuccinate lyase / argininosuccinate lyase activity / arginine metabolic process / Urea cycle / arginine biosynthetic process via ornithine / urea cycle / arginine biosynthetic process / post-embryonic development / locomotory behavior / positive regulation of nitric oxide biosynthetic process / extracellular exosome / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
Argininosuccinate lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsTurner, M.A. / Simpson, A. / Mcinnes, R.R. / Howell, P.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Human argininosuccinate lyase: a structural basis for intragenic complementation.
Authors: Turner, M.A. / Simpson, A. / McInnes, R.R. / Howell, P.L.
History
DepositionJul 10, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGININOSUCCINATE LYASE
B: ARGININOSUCCINATE LYASE


Theoretical massNumber of molelcules
Total (without water)103,9522
Polymers103,9522
Non-polymers00
Water00
1
A: ARGININOSUCCINATE LYASE
B: ARGININOSUCCINATE LYASE

A: ARGININOSUCCINATE LYASE
B: ARGININOSUCCINATE LYASE


Theoretical massNumber of molelcules
Total (without water)207,9054
Polymers207,9054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area28580 Å2
ΔGint-154 kcal/mol
Surface area55540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.600, 104.600, 183.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2466, 0.7165, -0.6525), (0.7166, -0.5881, -0.375), (-0.6525, -0.3751, -0.6585)
Vector: 46.124, 28.023, 118.812)

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Components

#1: Protein ARGININOSUCCINATE LYASE


Mass: 51976.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Organ: LIVER / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04424, argininosuccinate lyase

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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: 2.9 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.1 / Details: PROTEIN CRYSTALLIZED FROM 1.1M PHOSPHATE, pH 7.1
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
250 mMphosphate1drop
35 mMdithiothreitol1drop
41.1 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1994 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4→15 Å / Num. obs: 23049 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 2.66 % / Rsym value: 0.116
Reflection
*PLUS
Num. obs: 8659 / Num. measured all: 23049 / Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -8 %RANDOM
Rwork0.1879 ---
obs0.1879 6474 --
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 4.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6788 0 0 0 6788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.386
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.46
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.276
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 4.2→4.36 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.27 56 8.6 %
Rwork0.16 647 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.46
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.276
LS refinement shell
*PLUS
Rfactor obs: 0.16

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