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- PDB-6aef: PapA2 acyl transferase -

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Basic information

Entry
Database: PDB / ID: 6aef
TitlePapA2 acyl transferase
ComponentsTrehalose-2-sulfate acyltransferase PapA2
KeywordsTRANSFERASE / Mycobacterium tuberculesis PapA2 Acyl transferase Polyketide synthase associated protein
Function / homology
Function and homology information


2-O-sulfo trehalose long-chain-acyltransferase / sulfolipid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / catalytic activity / cell wall organization
Similarity search - Function
Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Trehalose-2-sulfate acyltransferase PapA2 / Polyketide synthase associated protein PapA2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsChaudhary, S. / Rao, V. / Panchal, V.
Funding support India, 3items
OrganizationGrant numberCountry
DST SERB Ramanujan Fellowship SB/S2/RJN-14/2013 dt. 3.9.13 India
CSIR BSC 0123 India
UGC doctoral fellowship India
CitationJournal: Faseb Bioadv / Year: 2019
Title: A novel mutation alters the stability of PapA2 resulting in the complete abrogation of sulfolipids in clinical mycobacterial strains.
Authors: Panchal, V. / Jatana, N. / Malik, A. / Taneja, B. / Pal, R. / Bhatt, A. / Besra, G.S. / Thukral, L. / Chaudhary, S. / Rao, V.
History
DepositionAug 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Trehalose-2-sulfate acyltransferase PapA2
A: Trehalose-2-sulfate acyltransferase PapA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6646
Polymers104,3522
Non-polymers3124
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area37940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.707, 100.668, 128.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Trehalose-2-sulfate acyltransferase PapA2 / Polyketide synthase-associated protein A2


Mass: 52175.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: papA2, Rv3820c / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P9WIK7, UniProt: R4MC47*PLUS, 2-O-sulfo trehalose long-chain-acyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.33 Å3/Da / Density % sol: 47.26 % / Description: sheets
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, magnesium chloride, sodium cacodylate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97883 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.16→39.714 Å / Num. obs: 52880 / % possible obs: 99.5 % / Redundancy: 6.5 % / Net I/σ(I): 2.24
Reflection shellResolution: 2.16→2.25 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.16→39.714 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2315 2620 5.03 %
Rwork0.1981 --
obs0.1998 52058 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.16→39.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 14 472 7692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057428
X-RAY DIFFRACTIONf_angle_d0.71110137
X-RAY DIFFRACTIONf_dihedral_angle_d10.1464403
X-RAY DIFFRACTIONf_chiral_restr0.0461124
X-RAY DIFFRACTIONf_plane_restr0.0051332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1596-2.19890.29831230.25652304X-RAY DIFFRACTION88
2.1989-2.24120.45651120.34882372X-RAY DIFFRACTION92
2.2412-2.28690.37491260.36232398X-RAY DIFFRACTION92
2.2869-2.33670.2951330.23032649X-RAY DIFFRACTION100
2.3367-2.3910.25281320.21682588X-RAY DIFFRACTION100
2.391-2.45080.26721220.22172628X-RAY DIFFRACTION100
2.4508-2.51710.28311470.21082626X-RAY DIFFRACTION100
2.5171-2.59110.22861410.21842597X-RAY DIFFRACTION100
2.5911-2.67470.29941640.22162587X-RAY DIFFRACTION100
2.6747-2.77030.24821420.22072621X-RAY DIFFRACTION100
2.7703-2.88120.25271480.20992631X-RAY DIFFRACTION100
2.8812-3.01230.2411410.20372605X-RAY DIFFRACTION100
3.0123-3.1710.24681290.19692638X-RAY DIFFRACTION100
3.171-3.36960.24091410.19542658X-RAY DIFFRACTION100
3.3696-3.62960.19471410.1822651X-RAY DIFFRACTION100
3.6296-3.99460.19721390.17242651X-RAY DIFFRACTION100
3.9946-4.57190.1931490.162679X-RAY DIFFRACTION100
4.5719-5.75730.19551600.16332703X-RAY DIFFRACTION100
5.7573-39.72040.20141300.19172852X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.62960.1995-0.31761.10410.54212.4506-0.01760.0470.08420.0177-0.01630.0684-0.1824-0.19760.03370.21640.0255-0.01940.23850.02690.2627-6.432635.6894-12.8716
21.58280.4432-0.2081.4547-0.00390.5956-0.1203-0.0797-0.1715-0.07290.0319-0.05350.14560.02510.09450.33360.01060.02230.31150.01090.3334-7.350512.5806-18.9212
31.31790.6461-0.54642.183-0.45471.6661-0.1218-0.1129-0.1519-0.1177-0.0405-0.170.09760.18810.12630.18430.03380.02640.26360.04690.272137.275337.1344-35.8606
40.98210.0867-0.18280.0238-0.11580.6317-0.26760.2201-0.4391-0.60340.1156-0.56540.212-0.13480.10280.4416-0.07810.22650.253-0.05750.396221.097322.0624-38.678
52.5621.1195-0.79661.0497-0.18330.7703-0.62620.8203-0.1425-0.5940.49350.02240.3607-0.27830.02240.5797-0.2330.07220.5848-0.03980.397516.352424.3349-50.5323
62.9510.44350.80671.0148-0.41261.5734-0.73791.0711-0.1358-0.56760.4134-0.10110.3673-0.2245-0.39160.6706-0.2880.1490.7056-0.03930.431827.401628.9813-57.956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 234 )
2X-RAY DIFFRACTION2chain 'B' and (resid 235 through 459 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 189 )
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 397 )
6X-RAY DIFFRACTION6chain 'A' and (resid 398 through 459 )

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