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- PDB-6p1y: Crystal structure of Mtb aspartate decarboxylase mutant M117I -

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Basic information

Entry
Database: PDB / ID: 6p1y
TitleCrystal structure of Mtb aspartate decarboxylase mutant M117I
Components
  • Aspartate 1-decarboxylase alpha chain
  • Aspartate 1-decarboxylase beta chain
KeywordsLYASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / POA / drug-resistance / mutant
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / peptidoglycan-based cell wall / cytosol
Similarity search - Function
Aspartate decarboxylase / Aspartate decarboxylase / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
AMMONIUM ION / L(+)-TARTARIC ACID / Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsSun, Q. / Li, X. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Welch FoundationA-0015 United States
CitationJournal: Nat Commun / Year: 2020
Title: The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD.
Authors: Sun, Q. / Li, X. / Perez, L.M. / Shi, W. / Zhang, Y. / Sacchettini, J.C.
History
DepositionMay 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate 1-decarboxylase beta chain
B: Aspartate 1-decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1234
Polymers15,9552
Non-polymers1682
Water70339
1
A: Aspartate 1-decarboxylase beta chain
B: Aspartate 1-decarboxylase alpha chain
hetero molecules

A: Aspartate 1-decarboxylase beta chain
B: Aspartate 1-decarboxylase alpha chain
hetero molecules

A: Aspartate 1-decarboxylase beta chain
B: Aspartate 1-decarboxylase alpha chain
hetero molecules

A: Aspartate 1-decarboxylase beta chain
B: Aspartate 1-decarboxylase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,49316
Polymers63,8208
Non-polymers6738
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area26570 Å2
ΔGint-96 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.011, 73.011, 109.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein/peptide Aspartate 1-decarboxylase beta chain


Mass: 2751.341 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: panD, Rv3601c, MTCY07H7B.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIL3, aspartate 1-decarboxylase
#2: Protein Aspartate 1-decarboxylase alpha chain / Aspartate alpha-decarboxylase


Mass: 13203.739 Da / Num. of mol.: 1 / Mutation: M117I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: panD, Rv3601c, MTCY07H7B.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIL3, aspartate 1-decarboxylase
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: Ammonium tartrate dibasic, PEG 3350 / PH range: 6.5-7

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Data collection

DiffractionMean temperature: 130 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.33→36.51 Å / Num. obs: 6635 / % possible obs: 99.58 % / Redundancy: 11.3 % / Net I/σ(I): 18.88
Reflection shellResolution: 2.33→2.414 Å / Mean I/σ(I) obs: 3.75 / Num. unique obs: 636 / % possible all: 96.95

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C45

2c45


Resolution: 2.33→36.51 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.78
RfactorNum. reflection% reflection
Rfree0.2038 330 4.97 %
Rwork0.1743 --
obs0.1758 6634 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.6 Å2 / Biso mean: 38.8028 Å2 / Biso min: 20.82 Å2
Refinement stepCycle: final / Resolution: 2.33→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 11 39 995
Biso mean--65.04 43.44 -
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.33-2.93490.2361550.1836307399
2.9349-36.510.19261750.17113231100
Refinement TLS params.Method: refined / Origin x: -27.8584 Å / Origin y: -22.3682 Å / Origin z: -18.0447 Å
111213212223313233
T0.2657 Å2-0.0291 Å20.0097 Å2-0.269 Å2-0.0041 Å2--0.2976 Å2
L0.827 °20.4312 °20.2444 °2-1.2537 °2-0.4411 °2--1.4583 °2
S0.0052 Å °-0.0075 Å °0.1033 Å °0.0259 Å °0.034 Å °-0.0591 Å °-0.181 Å °0.099 Å °-0.0325 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 24
2X-RAY DIFFRACTION1allB25 - 126
3X-RAY DIFFRACTION1allS1 - 71
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1

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