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- PDB-6iga: Crystal structure of argininosuccinate lyase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 6iga
TitleCrystal structure of argininosuccinate lyase from Mycobacterium tuberculosis
ComponentsArgininosuccinate lyase
KeywordsLYASE / argininosuccinate lyase / fumarate / tetramer
Function / homology
Function and homology information


argininosuccinate lyase / argininosuccinate lyase activity / arginine biosynthetic process via ornithine / peptidoglycan-based cell wall / cytosol
Similarity search - Function
Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase, conserved site ...Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Argininosuccinate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.776 Å
AuthorsChen, X.B. / Liu, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China813300237 China
National Natural Science Foundation of China81520108019 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure and biochemical study on argininosuccinate lyase from Mycobacterium tuberculosis.
Authors: Chen, X.B. / Chen, J. / Zhang, W. / Wang, H. / Liu, X. / Zhou, W. / Yang, H. / Rao, Z.
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Argininosuccinate lyase
D: Argininosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,4095
Polymers199,3134
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28860 Å2
ΔGint-166 kcal/mol
Surface area57440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.155, 129.155, 200.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Argininosuccinate lyase / ASAL / Arginosuccinase


Mass: 49828.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: argH, Rv1659, MTCY06H11.24 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPY7, argininosuccinate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium tartrate dibasic, pH 7.0, 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 2.776→50 Å / Num. obs: 43973 / % possible obs: 95.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 7.66
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.443 / Num. unique obs: 2273

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HY1

1hy1


Resolution: 2.776→45.673 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 2170 4.93 %
Rwork0.219 --
obs0.2208 43973 88.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.776→45.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13588 0 5 0 13593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613824
X-RAY DIFFRACTIONf_angle_d0.94218802
X-RAY DIFFRACTIONf_dihedral_angle_d13.5264996
X-RAY DIFFRACTIONf_chiral_restr0.0462180
X-RAY DIFFRACTIONf_plane_restr0.0042504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.776-2.84050.3421030.2721565X-RAY DIFFRACTION51
2.8405-2.91160.28951150.27052312X-RAY DIFFRACTION74
2.9116-2.99030.35491360.2772510X-RAY DIFFRACTION81
2.9903-3.07820.28511460.26382671X-RAY DIFFRACTION86
3.0782-3.17760.34361470.26742786X-RAY DIFFRACTION91
3.1776-3.29110.33921630.26912911X-RAY DIFFRACTION94
3.2911-3.42280.29731280.25492993X-RAY DIFFRACTION95
3.4228-3.57860.31291500.24252940X-RAY DIFFRACTION94
3.5786-3.76710.26051250.23992999X-RAY DIFFRACTION95
3.7671-4.0030.25321540.212987X-RAY DIFFRACTION96
4.003-4.31190.2171360.19223058X-RAY DIFFRACTION97
4.3119-4.74540.20831720.17683007X-RAY DIFFRACTION96
4.7454-5.43110.22051800.19572997X-RAY DIFFRACTION95
5.4311-6.8390.25551420.21823093X-RAY DIFFRACTION96
6.839-45.6790.19571730.17532974X-RAY DIFFRACTION90

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