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- PDB-9ggj: Crystal structure of argininosuccinate lyase from Arabidopsis tha... -

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Basic information

Entry
Database: PDB / ID: 9ggj
TitleCrystal structure of argininosuccinate lyase from Arabidopsis thaliana (AtASL) in complex with biological substrate and products - argininosuccinate, argnine and fumarate
ComponentsArgininosuccinate lyase, chloroplastic
KeywordsLYASE / arginine / urea cycle / complex / argininosuccinate
Function / homology
Function and homology information


argininosuccinate lyase / argininosuccinate lyase activity / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / chloroplast stroma / chloroplast
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
ARGININE / ARGININOSUCCINATE / FUMARIC ACID / Argininosuccinate lyase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNielipinski, M. / Pietrzyk-Brzezinska, A.J. / Krzeszewska, D. / Sekula, B.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA17 2021/43/D/NZ1/00486 Poland
CitationJournal: J.Struct.Biol. / Year: 2024
Title: Arabidopsis thaliana argininosuccinate lyase structure uncovers the role of serine as the catalytic base.
Authors: Nielipinski, M. / Nielipinska, D. / Pietrzyk-Brzezinska, A.J. / Sekula, B.
History
DepositionAug 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Argininosuccinate lyase, chloroplastic
B: Argininosuccinate lyase, chloroplastic
C: Argininosuccinate lyase, chloroplastic
D: Argininosuccinate lyase, chloroplastic
E: Argininosuccinate lyase, chloroplastic
F: Argininosuccinate lyase, chloroplastic
G: Argininosuccinate lyase, chloroplastic
H: Argininosuccinate lyase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,16055
Polymers415,8328
Non-polymers5,32747
Water53,2702957
1
A: Argininosuccinate lyase, chloroplastic
B: Argininosuccinate lyase, chloroplastic
C: Argininosuccinate lyase, chloroplastic
D: Argininosuccinate lyase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,57829
Polymers207,9164
Non-polymers2,66125
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35090 Å2
ΔGint-358 kcal/mol
Surface area56410 Å2
2
E: Argininosuccinate lyase, chloroplastic
F: Argininosuccinate lyase, chloroplastic
G: Argininosuccinate lyase, chloroplastic
H: Argininosuccinate lyase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,58226
Polymers207,9164
Non-polymers2,66622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35830 Å2
ΔGint-353 kcal/mol
Surface area56430 Å2
Unit cell
Length a, b, c (Å)106.588, 230.848, 112.534
Angle α, β, γ (deg.)90.00, 89.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Argininosuccinate lyase, chloroplastic / Arginosuccinase


Mass: 51979.062 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g10920, T30N20.190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LEU8, argininosuccinate lyase

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Non-polymers , 7 types, 3004 molecules

#2: Chemical
ChemComp-AS1 / ARGININOSUCCINATE


Mass: 290.273 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H18N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N4O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2957 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.33 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0M Ammonium sulfate, pH 5.5 0.1 M Bis-TRIS, crystal soaked for 20 minutes in 20mM solution of argininosuccinate in mother liquor and 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→49.573 Å / Num. obs: 260782 / % possible obs: 90.38 % / Redundancy: 4.25 % / CC1/2: 0.9859 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.116 / Net I/σ(I): 4.25
Reflection shellResolution: 2→2.114 Å / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 13043 / CC1/2: 0.54 / Rpim(I) all: 0.459 / % possible all: 70.11

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.57 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.457 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22689 1974 0.8 %RANDOM
Rwork0.17544 ---
obs0.17583 258807 71.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.534 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å2-0 Å2-0.02 Å2
2---0.06 Å20 Å2
3---1.02 Å2
Refinement stepCycle: 1 / Resolution: 2→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28384 0 142 2957 31483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01229375
X-RAY DIFFRACTIONr_bond_other_d0.0010.01628041
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.83139804
X-RAY DIFFRACTIONr_angle_other_deg0.5811.7764705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10253715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.465221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.763105276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.24538
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0234673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026627
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6541.7614529
X-RAY DIFFRACTIONr_mcbond_other1.6541.7614530
X-RAY DIFFRACTIONr_mcangle_it2.6273.15618178
X-RAY DIFFRACTIONr_mcangle_other2.6273.15618178
X-RAY DIFFRACTIONr_scbond_it2.7612.11514846
X-RAY DIFFRACTIONr_scbond_other2.652.08114737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2953.67121403
X-RAY DIFFRACTIONr_long_range_B_refined6.72519.335626
X-RAY DIFFRACTIONr_long_range_B_other6.61418.1534899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 19 -
Rwork0.259 3624 -
obs--13.54 %
Refinement TLS params.Method: refined / Origin x: 47.984 Å / Origin y: -21.804 Å / Origin z: 28.826 Å
111213212223313233
T0.0017 Å20.0036 Å20.0046 Å2-0.0879 Å2-0.0122 Å2--0.1406 Å2
L0.0168 °2-0.0034 °20.0064 °2-0.1281 °2-0.0726 °2--0.0888 °2
S-0.0052 Å °-0.0036 Å °-0.0016 Å °0.0016 Å °-0.0073 Å °0.0098 Å °-0.0025 Å °0.0117 Å °0.0125 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 139
2X-RAY DIFFRACTION1A140 - 402
3X-RAY DIFFRACTION1A403 - 436
4X-RAY DIFFRACTION1A437 - 517
5X-RAY DIFFRACTION1B64 - 103
6X-RAY DIFFRACTION1B104 - 127
7X-RAY DIFFRACTION1B128 - 164
8X-RAY DIFFRACTION1B165 - 246
9X-RAY DIFFRACTION1B247 - 315
10X-RAY DIFFRACTION1B316 - 407
11X-RAY DIFFRACTION1B408 - 436
12X-RAY DIFFRACTION1B437 - 474
13X-RAY DIFFRACTION1B475 - 515
14X-RAY DIFFRACTION1C68 - 103
15X-RAY DIFFRACTION1C104 - 139
16X-RAY DIFFRACTION1C140 - 164
17X-RAY DIFFRACTION1C165 - 315
18X-RAY DIFFRACTION1C316 - 342
19X-RAY DIFFRACTION1C343 - 402
20X-RAY DIFFRACTION1C403 - 436
21X-RAY DIFFRACTION1C437 - 474
22X-RAY DIFFRACTION1C475 - 515
23X-RAY DIFFRACTION1D68 - 139
24X-RAY DIFFRACTION1D140 - 407
25X-RAY DIFFRACTION1D408 - 436
26X-RAY DIFFRACTION1D437 - 515
27X-RAY DIFFRACTION1E67 - 139
28X-RAY DIFFRACTION1E140 - 164
29X-RAY DIFFRACTION1E165 - 402
30X-RAY DIFFRACTION1E403 - 436
31X-RAY DIFFRACTION1E437 - 517
32X-RAY DIFFRACTION1F62 - 103
33X-RAY DIFFRACTION1F104 - 139
34X-RAY DIFFRACTION1F140 - 316
35X-RAY DIFFRACTION1F317 - 342
36X-RAY DIFFRACTION1F343 - 436
37X-RAY DIFFRACTION1F437 - 482
38X-RAY DIFFRACTION1F483 - 515
39X-RAY DIFFRACTION1G68 - 139
40X-RAY DIFFRACTION1G140 - 164
41X-RAY DIFFRACTION1G165 - 315
42X-RAY DIFFRACTION1G316 - 342
43X-RAY DIFFRACTION1G343 - 436
44X-RAY DIFFRACTION1G437 - 515
45X-RAY DIFFRACTION1H68 - 127
46X-RAY DIFFRACTION1H128 - 164
47X-RAY DIFFRACTION1H165 - 407
48X-RAY DIFFRACTION1H408 - 436
49X-RAY DIFFRACTION1H437 - 482
50X-RAY DIFFRACTION1H483 - 515

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