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- PDB-5ocj: Crystal structure of Ag85C bound to cyclophostin 8beta inhibitor -

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Basic information

Entry
Database: PDB / ID: 5ocj
TitleCrystal structure of Ag85C bound to cyclophostin 8beta inhibitor
ComponentsDiacylglycerol acyltransferase/mycolyltransferase Ag85C
KeywordsTRANSFERASE / Ag85C / mycolicate / mycomembrane / TMM / TDM
Function / homology
Function and homology information


trehalose O-mycolyltransferase activity / trehalose O-mycolyltransferase / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / mycolate cell wall layer assembly / glycolipid biosynthetic process / zymogen binding / acyltransferase activity, transferring groups other than amino-acyl groups / lipid transport / peptidoglycan-based cell wall ...trehalose O-mycolyltransferase activity / trehalose O-mycolyltransferase / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / mycolate cell wall layer assembly / glycolipid biosynthetic process / zymogen binding / acyltransferase activity, transferring groups other than amino-acyl groups / lipid transport / peptidoglycan-based cell wall / response to antibiotic / extracellular region / membrane
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9SW / Diacylglycerol acyltransferase/mycolyltransferase Ag85C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsViljoen, A. / Richard, M. / Nguyen, P.C. / Spilling, C.D. / Canaan, S. / Cavalier, J.F. / Blaise, M. / Kremer, L.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Cyclipostins and cyclophostin analogs inhibit the antigen 85C from
Authors: Viljoen, A. / Richard, M. / Nguyen, P.C. / Fourquet, P. / Camoin, L. / Paudal, R.R. / Gnawali, G.R. / Spilling, C.D. / Cavalier, J.F. / Canaan, S. / Blaise, M. / Kremer, L.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: 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: Diacylglycerol acyltransferase/mycolyltransferase Ag85C
B: Diacylglycerol acyltransferase/mycolyltransferase Ag85C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4836
Polymers66,4862
Non-polymers9974
Water9,602533
1
A: Diacylglycerol acyltransferase/mycolyltransferase Ag85C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7413
Polymers33,2431
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diacylglycerol acyltransferase/mycolyltransferase Ag85C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7413
Polymers33,2431
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.390, 75.770, 137.320
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 Diacylglycerol acyltransferase/mycolyltransferase Ag85C / DGAT / Acyl-CoA:diacylglycerol acyltransferase / Antigen 85 complex C / Ag85C / Fibronectin-binding ...DGAT / Acyl-CoA:diacylglycerol acyltransferase / Antigen 85 complex C / Ag85C / Fibronectin-binding protein C / Fbps C


Mass: 33242.785 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: fbpC, mpt45, Rv0129c, MTCI5.03c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P9WQN9, trehalose O-mycolyltransferase, diacylglycerol O-acyltransferase
#2: Chemical ChemComp-9SW / methoxy-[(3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]pentadecyl]phosphinic acid


Mass: 420.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41O6P
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5 and 10% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.8→48.095 Å / Num. obs: 65871 / % possible obs: 99.92 % / Redundancy: 8 % / Rrim(I) all: 0.09689 / Net I/σ(I): 16.66
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.24 / Num. unique obs: 6486 / CC1/2: 0.729 / Rpim(I) all: 0.372 / Rrim(I) all: 1.049 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HRH

3hrh


Resolution: 1.8→48.095 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1748 2000 3.04 %
Rwork0.1507 --
obs0.1514 65862 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→48.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 54 533 4884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064501
X-RAY DIFFRACTIONf_angle_d0.8216152
X-RAY DIFFRACTIONf_dihedral_angle_d13.5212562
X-RAY DIFFRACTIONf_chiral_restr0.056613
X-RAY DIFFRACTIONf_plane_restr0.006815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.26821410.23774507X-RAY DIFFRACTION100
1.845-1.89490.21951400.20584475X-RAY DIFFRACTION100
1.8949-1.95070.2241420.18864521X-RAY DIFFRACTION100
1.9507-2.01360.21231410.17434496X-RAY DIFFRACTION100
2.0136-2.08560.19111410.15624502X-RAY DIFFRACTION100
2.0856-2.16910.18881420.14824544X-RAY DIFFRACTION100
2.1691-2.26780.18031420.14764516X-RAY DIFFRACTION100
2.2678-2.38740.19111410.14854518X-RAY DIFFRACTION100
2.3874-2.5370.19561430.1594572X-RAY DIFFRACTION100
2.537-2.73280.20421430.15974553X-RAY DIFFRACTION100
2.7328-3.00780.17371430.15444575X-RAY DIFFRACTION100
3.0078-3.44290.15911440.14344606X-RAY DIFFRACTION100
3.4429-4.33730.1351450.12474634X-RAY DIFFRACTION100
4.3373-48.11180.1641520.14664843X-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)
18.9472-6.6736-2.90045.69843.47842.9563-0.0302-0.01520.333-0.06510.2498-0.54070.0590.1932-0.23540.1681-0.0156-0.00920.2258-0.01620.201316.9519-21.9193-5.2548
23.1331.23150.70463.00290.30774.137-0.05920.18860.0988-0.25310.0492-0.16480.0086-0.09560.00980.14950.0399-0.01330.13120.00020.22567.4075-20.445-7.8332
31.72870.111-0.00661.1692-0.27242.05950.0371-0.07560.1414-0.0541-0.0610.0252-0.1538-0.07540.00750.14060.0004-0.00280.1537-0.01810.16995.1291-18.2431-6.6376
41.5583-0.3245-0.35652.883.66687.4150.00980.0386-0.0875-0.09620.09-0.1810.01230.3646-0.12740.1590.00810.00010.15650.02330.191913.3318-31.2097-6.1054
51.17-0.2205-0.46661.20140.64482.3840.00820.0851-0.0648-0.0744-0.0150.03370.189-0.12020.0120.1752-0.0189-0.00740.1719-0.00710.17230.0366-34.8008-13.224
61.663-0.0669-0.01052.3471-0.97093.7295-0.11660.02920.0645-0.05830.0088-0.0162-0.1168-0.36330.10660.1121-0.0076-0.0060.1895-0.05280.1807-9.4908-26.112-8.8183
71.92653.4181-3.62575.4511-5.80886.48470.09330.1230.078-0.30940.16080.56250.2948-0.5234-0.30760.2233-0.0049-0.01210.3378-0.0310.2792-12.8197-29.0769-15.8083
82.40150.2823-0.53561.75680.09833.0152-0.0195-0.21580.05610.1056-0.0060.1176-0.0856-0.29680.0260.10870.0263-0.00440.1894-0.03440.171-8.864-20.5549-4.9489
98.89083.9155-3.78275.2854-1.94114.3142-0.01040.30620.576-0.34460.20240.4498-0.205-0.1684-0.24870.32270.033-0.11310.21150.01930.244-18.7458-12.8358-53.8066
102.48480.0733-1.19595.3385-0.74121.833-0.01640.03660.0963-0.2978-0.01430.0669-0.0815-0.12290.00710.1864-0.0214-0.0460.14410.02220.1771-11.935-18.6992-50.23
112.21210.16930.57332.71330.19451.7643-0.04160.15820.08-0.456-0.0943-0.1268-0.05220.14980.12640.25670.0123-0.0080.14840.01830.1651-9.0906-19.4009-51.7653
122.7958-0.1341-0.57242.7042-0.3966.3326-0.1134-0.02940.1089-0.2147-0.1650.511-0.3036-0.37330.23050.20710.0114-0.10140.1966-0.03140.327-24.2413-21.0345-49.3159
131.7104-0.3043-0.45592.48580.52913.2273-0.05-0.1894-0.0760.1139-0.07890.2120.0999-0.11310.14040.2131-0.0104-0.00620.20390.00280.2215-17.2173-31.4495-40.274
142.75521.36841.30523.8711.613.2381-0.04630.0828-0.025-0.1339-0.0044-0.20140.00090.28420.03720.21020.04160.02650.18010.04310.2293-5.1773-34.7831-46.1887
157.58663.82685.85032.15342.47385.12850.1296-0.3515-0.29180.1446-0.0912-0.27540.2369-0.1161-0.05310.2390.01730.02680.23040.05650.1949-4.2737-37.2429-38.3368
161.02030.0789-0.16744.22970.90811.82710.02080.138-0.0904-0.4331-0.0688-0.41260.03910.18930.0310.21240.0370.05180.22090.0360.2308-2.1338-31.8668-51.4845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 192 )
6X-RAY DIFFRACTION6chain 'A' and (resid 193 through 221 )
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 244 )
8X-RAY DIFFRACTION8chain 'A' and (resid 245 through 282 )
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 27 )
10X-RAY DIFFRACTION10chain 'B' and (resid 28 through 47 )
11X-RAY DIFFRACTION11chain 'B' and (resid 48 through 79 )
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 118 )
13X-RAY DIFFRACTION13chain 'B' and (resid 119 through 192 )
14X-RAY DIFFRACTION14chain 'B' and (resid 193 through 221 )
15X-RAY DIFFRACTION15chain 'B' and (resid 222 through 244 )
16X-RAY DIFFRACTION16chain 'B' and (resid 245 through 282 )

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