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- PDB-3pty: Crystal structure of the C-terminal extracellular domain of Mycob... -

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Basic information

Entry
Database: PDB / ID: 3pty
TitleCrystal structure of the C-terminal extracellular domain of Mycobacterium tuberculosis EmbC
ComponentsArabinosyltransferase C
KeywordsTRANSFERASE / beta-sandwich / carbohydrate binding / carbohydrate
Function / homology
Function and homology information


arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / glycolipid biosynthetic process / Transferases; Glycosyltransferases; Pentosyltransferases / membrane => GO:0016020 / cell wall organization / response to antibiotic / plasma membrane / cytosol
Similarity search - Function
EmbC, C-terminal domain, subdomain 2 / D-Maltodextrin-Binding Protein; domain 2 - #160 / Arabinofuranosyltransferase, central domain / Arabinofuranosyltransferase, domain 1 / Arabinosyltransferase, C-terminal / Arabinosyltransferas, concanavalin like domain / Arabinosyltransferase, C-terminal, subdomain 2 / Mycobacterial cell wall arabinan synthesis protein / EmbC C-terminal domain / Arabinosyltransferase concanavalin like domain ...EmbC, C-terminal domain, subdomain 2 / D-Maltodextrin-Binding Protein; domain 2 - #160 / Arabinofuranosyltransferase, central domain / Arabinofuranosyltransferase, domain 1 / Arabinosyltransferase, C-terminal / Arabinosyltransferas, concanavalin like domain / Arabinosyltransferase, C-terminal, subdomain 2 / Mycobacterial cell wall arabinan synthesis protein / EmbC C-terminal domain / Arabinosyltransferase concanavalin like domain / D-Maltodextrin-Binding Protein; domain 2 / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
octyl alpha-D-arabinofuranoside / PHOSPHATE ION / Probable arabinosyltransferase C / Probable arabinosyltransferase C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsAlderwick, L.J. / Besra, G.S. / Futterer, K.
CitationJournal: Plos Pathog. / Year: 2011
Title: The C-Terminal Domain of the Arabinosyltransferase Mycobacterium tuberculosis EmbC Is a Lectin-Like Carbohydrate Binding Module.
Authors: Alderwick, L.J. / Lloyd, G.S. / Ghadbane, H. / May, J.W. / Bhatt, A. / Eggeling, L. / Futterer, K. / Besra, G.S.
History
DepositionDec 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.mon_nstd_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Arabinosyltransferase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9764
Polymers43,5791
Non-polymers3973
Water2,036113
1
A: Arabinosyltransferase C
hetero molecules

A: Arabinosyltransferase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9528
Polymers87,1582
Non-polymers7956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3230 Å2
ΔGint-56 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.130, 129.130, 136.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsDimerization may not occur in the context of the full length protein

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Components

#1: Protein Arabinosyltransferase C / Arabinosyltransferase EmbC


Mass: 43578.848 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 719-1094)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: embC, MT3900, MTCY13D12.27, Rv3793 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P72059, UniProt: P9WNL5*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Sugar ChemComp-AFO / octyl alpha-D-arabinofuranoside / octyl alpha-D-arabinoside / octyl D-arabinoside / octyl arabinoside


Type: D-saccharide / Mass: 262.343 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C13H26O5
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.78 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M sodium acetate, 0.08 M ammonium phosphate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763,0.9797,0.9799
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2006 / Details: mirrors
RadiationMonochromator: silicon(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.97971
30.97991
ReflectionResolution: 2→46.9 Å / Num. all: 45942 / Num. obs: 45942 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 27
Reflection shellResolution: 2→2.11 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 5.3 / Num. unique all: 6577 / Rsym value: 0.564 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDEphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→43.282 Å / SU ML: 0.25 / σ(F): 1.38 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 4348 5.05 %RANDOM
Rwork0.187 ---
obs0.188 43081 100 %-
all-43081 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.786 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0758 Å2-0 Å20 Å2
2---1.0758 Å2-0 Å2
3---2.1517 Å2
Refinement stepCycle: LAST / Resolution: 2→43.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 24 113 2258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062199
X-RAY DIFFRACTIONf_angle_d1.0523013
X-RAY DIFFRACTIONf_dihedral_angle_d17.683780
X-RAY DIFFRACTIONf_chiral_restr0.074341
X-RAY DIFFRACTIONf_plane_restr0.005395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.26811340.22662721X-RAY DIFFRACTION100
2.0227-2.04650.27841420.21632746X-RAY DIFFRACTION100
2.0465-2.07150.25011490.21162697X-RAY DIFFRACTION100
2.0715-2.09770.24511040.20752761X-RAY DIFFRACTION100
2.0977-2.12530.23681610.19712708X-RAY DIFFRACTION100
2.1253-2.15440.22951490.18752744X-RAY DIFFRACTION100
2.1544-2.18520.1871600.18282737X-RAY DIFFRACTION100
2.1852-2.21780.21671700.17452666X-RAY DIFFRACTION100
2.2178-2.25250.21951150.17412732X-RAY DIFFRACTION100
2.2525-2.28940.20081460.17622742X-RAY DIFFRACTION100
2.2894-2.32890.17361360.17372748X-RAY DIFFRACTION100
2.3289-2.37120.19331110.17142745X-RAY DIFFRACTION100
2.3712-2.41680.15561570.17692725X-RAY DIFFRACTION100
2.4168-2.46610.21051340.18832703X-RAY DIFFRACTION100
2.4661-2.51980.2221690.19842760X-RAY DIFFRACTION100
2.5198-2.57840.2291680.19432702X-RAY DIFFRACTION100
2.5784-2.64280.1941520.18122704X-RAY DIFFRACTION100
2.6428-2.71430.22971260.18452734X-RAY DIFFRACTION100
2.7143-2.79410.2041320.18162755X-RAY DIFFRACTION100
2.7941-2.88430.20581490.18092731X-RAY DIFFRACTION100
2.8843-2.98740.22261480.20082725X-RAY DIFFRACTION100
2.9874-3.1070.23021630.20362696X-RAY DIFFRACTION100
3.107-3.24830.23171330.19432752X-RAY DIFFRACTION100
3.2483-3.41950.20991500.19142728X-RAY DIFFRACTION100
3.4195-3.63370.2431380.18762715X-RAY DIFFRACTION100
3.6337-3.9140.17451600.17822751X-RAY DIFFRACTION100
3.914-4.30760.16971440.16412707X-RAY DIFFRACTION100
4.3076-4.93020.16291510.1462711X-RAY DIFFRACTION100
4.9302-6.20860.18011710.17592719X-RAY DIFFRACTION100
6.2086-43.29210.19511260.19372750X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 80.7989 Å / Origin y: 5.1276 Å / Origin z: 20.1224 Å
111213212223313233
T0.1643 Å2-0.0117 Å20.0128 Å2-0.1556 Å2-0.0171 Å2--0.1717 Å2
L0.4919 °2-0.2945 °2-0.6492 °2-0.5821 °20.3292 °2--0.8765 °2
S-0.0239 Å °-0.0248 Å °-0.0436 Å °0.0213 Å °-0.0174 Å °0.0812 Å °0.042 Å °0.069 Å °0 Å °
Refinement TLS groupSelection details: chain A

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