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- PDB-1k62: Crystal Structure of the Human Argininosuccinate Lyase Q286R Mutant -

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Basic information

Entry
Database: PDB / ID: 1k62
TitleCrystal Structure of the Human Argininosuccinate Lyase Q286R Mutant
ComponentsArgininosuccinate Lyase
KeywordsLYASE / intragenic complementation / arginiosuccinate lyase / delta crystallin / enzyme mechanism
Function / homology
Function and homology information


argininosuccinate lyase / argininosuccinate lyase activity / ammonia assimilation cycle / arginine metabolic process / Urea cycle / L-arginine biosynthetic process via ornithine / urea cycle / L-arginine biosynthetic process / post-embryonic development / locomotory behavior ...argininosuccinate lyase / argininosuccinate lyase activity / ammonia assimilation cycle / arginine metabolic process / Urea cycle / L-arginine biosynthetic process via ornithine / urea cycle / L-arginine biosynthetic process / post-embryonic development / locomotory behavior / positive regulation of nitric oxide biosynthetic process / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) ...Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Argininosuccinate lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSampaleanu, L.M. / Vallee, F. / Thompson, G.D. / Howell, P.L.
CitationJournal: Biochemistry / Year: 2001
Title: Three-dimensional structure of the argininosuccinate lyase frequently complementing allele Q286R.
Authors: Sampaleanu, L.M. / Vallee, F. / Thompson, G.D. / Howell, P.L.
History
DepositionOct 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Argininosuccinate Lyase
B: Argininosuccinate Lyase


Theoretical massNumber of molelcules
Total (without water)103,8682
Polymers103,8682
Non-polymers00
Water3,999222
1
A: Argininosuccinate Lyase
B: Argininosuccinate Lyase

A: Argininosuccinate Lyase
B: Argininosuccinate Lyase


Theoretical massNumber of molelcules
Total (without water)207,7374
Polymers207,7374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area30460 Å2
ΔGint-161.1 kcal/mol
Surface area58850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.202, 104.202, 183.019
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtriclinic
Space group name H-MP3121
DetailsThe biological assembly is a homotetramer generated from the dimer in the asymmetric unit by the operation: -x, y-x, 1/3-z

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Components

#1: Protein Argininosuccinate Lyase / E.C.4.3.2.1 / ARGINOSUCCINASE / ASAL


Mass: 51934.164 Da / Num. of mol.: 2 / Mutation: Q286R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04424, argininosuccinate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1 M phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
pH: 7.1
Details: Turner, M.A., (1997) Proc.Natl.Acad.Sci.USA, 94, 9063.
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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999
RadiationMonochromator: crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→17 Å / Num. all: 79294 / Num. obs: 79294 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.1 / Net I/σ(I): 8.1
Reflection shellResolution: 2.65→2.74 Å / Rsym value: 0.46 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 17 Å / Num. obs: 33242 / Num. measured all: 79294 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.46

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUW

1auw


Resolution: 2.65→16.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 8156643.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3208 10.2 %RANDOM
Rwork0.175 ---
all0.187 31478 --
obs0.175 31478 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.2174 Å2 / ksol: 0.310664 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å28.92 Å20 Å2
2--2.26 Å20 Å2
3----4.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.65→16.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7122 0 0 222 7344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 495 10.1 %
Rwork0.258 4391 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAMCIS_PEPTIDE.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 17 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rfree: 0.295 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.258

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