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- PDB-9oo0: Mycobacterium tuberculosis PurB -

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Basic information

Entry
Database: PDB / ID: 9oo0
TitleMycobacterium tuberculosis PurB
ComponentsAdenylosuccinate lyase
KeywordsLYASE / adenylosuccinate lyase / Mycobacterium tuberculosis
Function / homology
Function and homology information


adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / cytosol
Similarity search - Function
Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / L-Aspartase-like
Similarity search - Domain/homology
Adenylosuccinate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJaganathan, D. / Chen, K. / Li, Z. / Li, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Infect Dis. / Year: 2026
Title: Structure, Function, and Inhibition of Adenylosuccinate Lyase (ADSL) from Mycobacterium tuberculosis .
Authors: Singh, V. / Jaganathan, D. / Corro, J. / Chen, K. / Kumar Samrat, S. / Zhang, R. / Ma, M. / Battaile, K.P. / Li, Z. / Zhang, Q.Y. / Xiong, R. / Ojha, A.K. / Li, H.
History
DepositionMay 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1674
Polymers103,9832
Non-polymers1842
Water8,053447
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,3348
Polymers207,9654
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area29160 Å2
ΔGint-118 kcal/mol
Surface area60840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.940, 176.710, 67.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein Adenylosuccinate lyase / ASL / Adenylosuccinase


Mass: 51991.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: purB, Rv0777 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: I6XWA1, adenylosuccinate lyase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris hydrochloride, pH 8.5, 30 to 35 percent PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→88.36 Å / Num. obs: 99665 / % possible obs: 93.06 % / Redundancy: 2 % / Biso Wilson estimate: 24.37 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.0723 / Rpim(I) all: 0.0723 / Rrim(I) all: 0.102 / Net I/σ(I): 9.46
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 6613 / CC1/2: 0.597 / CC star: 0.865 / Rpim(I) all: 0.48 / Rrim(I) all: 0.68 / % possible all: 62.92

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→88.36 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 2496 5.01 %Random
Rwork0.1789 47346 --
obs0.1816 49842 93.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→88.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7172 0 12 447 7631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00777331
X-RAY DIFFRACTIONf_angle_d0.87369936
X-RAY DIFFRACTIONf_chiral_restr0.04691144
X-RAY DIFFRACTIONf_plane_restr0.01021309
X-RAY DIFFRACTIONf_dihedral_angle_d5.22721058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.2466770.20941643X-RAY DIFFRACTION59.43
2.14-2.180.28681150.22631871X-RAY DIFFRACTION67.71
2.18-2.230.31781190.22092054X-RAY DIFFRACTION73.74
2.23-2.280.27111140.21812303X-RAY DIFFRACTION83.26
2.28-2.340.26291460.20182589X-RAY DIFFRACTION92.52
2.34-2.40.28551490.21012735X-RAY DIFFRACTION97.33
2.4-2.470.24771270.20032787X-RAY DIFFRACTION99.52
2.47-2.550.27831460.19622803X-RAY DIFFRACTION100
2.55-2.650.24461750.18992758X-RAY DIFFRACTION100
2.65-2.750.25151550.18862807X-RAY DIFFRACTION100
2.75-2.880.26461380.19452817X-RAY DIFFRACTION100
2.88-3.030.26581500.19462839X-RAY DIFFRACTION100
3.03-3.220.25651540.19162804X-RAY DIFFRACTION99.97
3.22-3.470.20611500.17652829X-RAY DIFFRACTION99.97
3.47-3.820.22231360.162856X-RAY DIFFRACTION99.97
3.82-4.370.18811610.14392864X-RAY DIFFRACTION100
4.37-5.50.19971310.14952940X-RAY DIFFRACTION99.9
5.5-88.360.19411530.17113047X-RAY DIFFRACTION99.72

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