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- PDB-6iem: Argininosuccinate lyase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6iem
TitleArgininosuccinate lyase from Mycobacterium tuberculosis
ComponentsArgininosuccinate lyase
KeywordsLYASE / arginine biosynthesis / mycobacterium tuberculosis / tetramer / aspartase/fumarase
Function / homology
Function and homology information


argininosuccinate lyase / argininosuccinate lyase activity / : / 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. / Fumarase/aspartase (N-terminal domain) / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase ...Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarase/aspartase (N-terminal domain) / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / 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
3,6,9,12,15-PENTAOXAHEPTADECANE / TRIETHYLENE GLYCOL / Argininosuccinate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 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
E: Argininosuccinate lyase
F: Argininosuccinate lyase
G: Argininosuccinate lyase
H: Argininosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,44722
Polymers398,6258
Non-polymers1,82214
Water12,268681
1
A: Argininosuccinate lyase
B: Argininosuccinate lyase
C: Argininosuccinate lyase
D: Argininosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,44614
Polymers199,3134
Non-polymers1,13310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29240 Å2
ΔGint-130 kcal/mol
Surface area55350 Å2
MethodPISA
2
E: Argininosuccinate lyase
F: Argininosuccinate lyase
G: Argininosuccinate lyase
H: Argininosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,0018
Polymers199,3134
Non-polymers6894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27490 Å2
ΔGint-131 kcal/mol
Surface area56620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.550, 183.820, 190.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A19 - 60
2116B19 - 60
3116C19 - 60
4116D19 - 60
5116E19 - 60
6116F19 - 60
7116G19 - 60
8116H19 - 60
1216A75 - 99
2216B75 - 99
3216C75 - 99
4216D75 - 99
5216E75 - 99
6216F75 - 99
7216G75 - 99
8216H75 - 99
1316A110 - 280
2316B110 - 280
3316C110 - 280
4316D110 - 280
5316E110 - 280
6316F110 - 280
7316G110 - 280
8316H110 - 280
1416A287 - 421
2416B287 - 421
3416C287 - 421
4416D287 - 421
5416E287 - 421
6416F287 - 421
7416G287 - 421
8416H287 - 421
1516A427 - 460
2516B427 - 460
3516C427 - 460
4516D427 - 460
5516E427 - 460
6516F427 - 460
7516G427 - 460
8516H427 - 460

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999053, 0.030423, -0.031102), (0.032961, 0.062633, -0.997492), (-0.028399, -0.997573, -0.063576)95.01233, 33.45265, 38.67941
3given(-0.218265, 0.658239, 0.720473), (0.659149, -0.44498, 0.60623), (0.719641, 0.607218, -0.336754)33.38443, 2.1376, -38.16883
4given(0.214935, -0.692713, -0.688442), (-0.688313, -0.607528, 0.396402), (-0.692841, 0.388663, -0.607382)62.83621, 72.95818, 37.85425
5given(-0.249252, -0.580964, 0.774825), (0.639212, -0.699733, -0.319033), (0.727518, 0.415758, 0.545769)18.05295, 43.548, -83.29125
6given(0.250756, 0.528121, -0.811301), (-0.6926, -0.487653, -0.531508), (-0.676333, 0.695186, 0.243494)81.61296, 119.45708, 1.02214
7given(0.999899, -0.010283, 0.009803), (-0.007548, 0.20005, 0.979757), (-0.012036, -0.979732, 0.199952)-2.40955, -55.9009, 26.36582
8given(-0.998053, 0.05815, 0.022571), (0.054695, 0.989805, -0.13151), (-0.029988, -0.13002, -0.991058)93.56384, 2.45121, 92.96345

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Argininosuccinate lyase / ASAL / Arginosuccinase


Mass: 49828.156 Da / Num. of mol.: 8
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 , 7 types, 695 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 100mM Bis-Tris pH 5.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→40.48 Å / Num. obs: 226389 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.215 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 32796 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E9F

2e9f


Resolution: 2.2→40.48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.986 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24394 11347 5 %RANDOM
Rwork0.20313 ---
obs0.20518 214919 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.775 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2--1.83 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.2→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26207 0 121 681 27009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01926804
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.96836503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.30253609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48423.1561052
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.243153901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.77715225
X-RAY DIFFRACTIONr_chiral_restr0.0870.24327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120339
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.8313.36514466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9025.04218059
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7783.52812338
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.30228.5342005
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2890 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.335
2BLOOSE POSITIONAL0.445
3CLOOSE POSITIONAL0.285
4DLOOSE POSITIONAL0.335
5ELOOSE POSITIONAL0.345
6FLOOSE POSITIONAL0.365
7GLOOSE POSITIONAL0.355
8HLOOSE POSITIONAL0.345
1ALOOSE THERMAL4.110
2BLOOSE THERMAL5.5310
3CLOOSE THERMAL4.5210
4DLOOSE THERMAL5.110
5ELOOSE THERMAL7.0910
6FLOOSE THERMAL6.0310
7GLOOSE THERMAL6.0310
8HLOOSE THERMAL6.1910
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 851 -
Rwork0.323 15673 -
obs--99.89 %

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