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- PDB-6ien: Substrate/product bound Argininosuccinate lyase from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 6ien
TitleSubstrate/product bound Argininosuccinate lyase from Mycobacterium tuberculosis
ComponentsArgininosuccinate lyase
KeywordsLYASE / arginine biosynthesis / tetramer / aspartase/fumarase / concerted movement
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) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...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 / 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 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ARGININE / ARGININOSUCCINATE / FUMARIC ACID / DI(HYDROXYETHYL)ETHER / Argininosuccinate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPaul, A. / Mishra, A. / Surolia, A. / Vijayan, M.
CitationJournal: IUBMB Life / Year: 2019
Title: Structural studies on M. tuberculosis argininosuccinate lyase and its liganded complex: Insights into catalytic mechanism.
Authors: Paul, A. / Mishra, A. / Surolia, A. / Vijayan, M.
History
DepositionSep 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 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.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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)200,89115
Polymers199,3134
Non-polymers1,57911
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34840 Å2
ΔGint-94 kcal/mol
Surface area49620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.180, 131.350, 145.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPY7, argininosuccinate lyase

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Non-polymers , 6 types, 304 molecules

#2: Chemical ChemComp-AS1 / ARGININOSUCCINATE / Argininosuccinic acid


Mass: 290.273 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18N4O6
#3: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 2.1M DL-malic acid pH 7.0, 10% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→25.86 Å / Num. obs: 60527 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.257 / Net I/σ(I): 4.4
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8743 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→25.86 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.353 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 1.252 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29295 3056 5.1 %RANDOM
Rwork0.2465 ---
obs0.24887 57383 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.291 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å2-0 Å2
2---0.72 Å2-0 Å2
3----1.37 Å2
Refinement stepCycle: 1 / Resolution: 2.7→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12967 0 107 293 13367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913286
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212877
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.97318037
X-RAY DIFFRACTIONr_angle_other_deg0.827329421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94751733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39923.021566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62152070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.28715130
X-RAY DIFFRACTIONr_chiral_restr0.0670.22096
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115289
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023005
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_it1.1512.5046956
X-RAY DIFFRACTIONr_mcbond_other1.1512.5046955
X-RAY DIFFRACTIONr_mcangle_it1.9863.7488684
X-RAY DIFFRACTIONr_mcangle_other1.9863.7488685
X-RAY DIFFRACTIONr_scbond_it1.1082.636330
X-RAY DIFFRACTIONr_scbond_other1.1072.636330
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9433.8969354
X-RAY DIFFRACTIONr_long_range_B_refined3.7419.67415773
X-RAY DIFFRACTIONr_long_range_B_other3.7419.67615774
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 245 -
Rwork0.303 4105 -
obs--100 %

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