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- PDB-4ubt: Structure of the C93S variant of the 3-ketoacyl-CoA thiolase FadA... -

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Open data


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Basic information

Entry
Database: PDB / ID: 4ubt
TitleStructure of the C93S variant of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis in complex with a steroid and CoA.
ComponentsAcetyl-CoA acetyltransferase FadA5
KeywordsTRANSFERASE / degradative thiolase / steroid-complex
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / cholesterol catabolic process / fatty acid beta-oxidation / identical protein binding
Similarity search - Function
Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3G6 / COENZYME A / DI(HYDROXYETHYL)ETHER / Steroid 3-ketoacyl-CoA thiolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchaefer, C.M. / Kisker, C.
Funding support Germany, United States, 8items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
German Research FoundationFZ82 Germany
National Institutes of HealthAI092455 United States
National Institutes of HealthAI085349 United States
National Institutes of HealthAI065251 United States
National Institutes of HealthHL53306 United States
National Institutes of HealthRR021008 United States
NSFBIO1039771 United States
CitationJournal: Structure / Year: 2015
Title: FadA5 a Thiolase from Mycobacterium tuberculosis: A Steroid-Binding Pocket Reveals the Potential for Drug Development against Tuberculosis.
Authors: Schaefer, C.M. / Lu, R. / Nesbitt, N.M. / Schiebel, J. / Sampson, N.S. / Kisker, C.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 2.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase FadA5
B: Acetyl-CoA acetyltransferase FadA5
C: Acetyl-CoA acetyltransferase FadA5
D: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,37028
Polymers169,3234
Non-polymers5,04824
Water20,9151161
1
A: Acetyl-CoA acetyltransferase FadA5
B: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,41016
Polymers84,6612
Non-polymers2,74814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-69 kcal/mol
Surface area26520 Å2
MethodPISA
2
C: Acetyl-CoA acetyltransferase FadA5
hetero molecules

D: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,96112
Polymers84,6612
Non-polymers2,29910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_446-x-1,y-1/2,-z+11
Buried area7480 Å2
ΔGint-39 kcal/mol
Surface area25280 Å2
MethodPISA
3
D: Acetyl-CoA acetyltransferase FadA5
hetero molecules

C: Acetyl-CoA acetyltransferase FadA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,96112
Polymers84,6612
Non-polymers2,29910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y+1/2,-z+11
Buried area7480 Å2
ΔGint-39 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.660, 100.180, 107.950
Angle α, β, γ (deg.)90.00, 99.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acetyl-CoA acetyltransferase FadA5 / Probable acetyl-CoA acetyltransferase FadA5 (Acetoacetyl-CoA thiolase)


Mass: 42330.656 Da / Num. of mol.: 4 / Mutation: C93S
Source method: isolated from a genetically manipulated source
Details: C93S variant of FadA5 in complex with a steroid-CoA
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: fadA5, Rv3546, P425_03688, RVBD_3546 / Plasmid: pSD31
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: I6XHI4, acetyl-CoA C-acyltransferase

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Non-polymers , 7 types, 1185 molecules

#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-3G6 / (2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-dimethyl-3-oxo-2,3,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]propanoic acid (non-preferred name)


Mass: 344.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H32O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 0.1 M Mes, 23% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91842 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 1.7→47.49 Å / Num. obs: 175728 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ubv
Resolution: 1.7→37.684 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1737 8795 5.01 %
Rwork0.1446 --
obs0.1461 175672 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11525 0 315 1161 13001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712558
X-RAY DIFFRACTIONf_angle_d1.09617149
X-RAY DIFFRACTIONf_dihedral_angle_d15.2314736
X-RAY DIFFRACTIONf_chiral_restr0.0771938
X-RAY DIFFRACTIONf_plane_restr0.0052266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.2762870.23245487X-RAY DIFFRACTION100
1.7193-1.73950.29782730.2275611X-RAY DIFFRACTION100
1.7395-1.76080.24873210.21725537X-RAY DIFFRACTION100
1.7608-1.7830.25282480.20025552X-RAY DIFFRACTION99
1.783-1.80650.23122980.19665519X-RAY DIFFRACTION100
1.8065-1.83130.2173110.18565537X-RAY DIFFRACTION99
1.8313-1.85740.19542860.17455425X-RAY DIFFRACTION98
1.8574-1.88510.18472730.16625523X-RAY DIFFRACTION99
1.8851-1.91460.20722840.165606X-RAY DIFFRACTION100
1.9146-1.9460.20342810.165532X-RAY DIFFRACTION100
1.946-1.97950.20962790.15585577X-RAY DIFFRACTION100
1.9795-2.01550.18922890.1495597X-RAY DIFFRACTION100
2.0155-2.05430.20753040.1495522X-RAY DIFFRACTION100
2.0543-2.09620.17943330.14425545X-RAY DIFFRACTION100
2.0962-2.14180.20022730.14415583X-RAY DIFFRACTION100
2.1418-2.19160.17052920.1415583X-RAY DIFFRACTION100
2.1916-2.24640.17812990.13795522X-RAY DIFFRACTION100
2.2464-2.30710.16882800.14155553X-RAY DIFFRACTION100
2.3071-2.3750.18882890.14275558X-RAY DIFFRACTION99
2.375-2.45170.1713180.13965519X-RAY DIFFRACTION100
2.4517-2.53930.18042880.14335583X-RAY DIFFRACTION100
2.5393-2.64090.17983180.14095580X-RAY DIFFRACTION100
2.6409-2.76110.16962890.13775559X-RAY DIFFRACTION100
2.7611-2.90660.17372890.14035588X-RAY DIFFRACTION100
2.9066-3.08860.18452880.15095585X-RAY DIFFRACTION100
3.0886-3.3270.17153050.14255606X-RAY DIFFRACTION100
3.327-3.66150.15813330.13235526X-RAY DIFFRACTION99
3.6615-4.19080.132910.12215615X-RAY DIFFRACTION100
4.1908-5.27760.14512750.12095643X-RAY DIFFRACTION100
5.2776-37.69360.1553010.15245704X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.56110.7756-0.27070.45730.19481.7120.1212-0.1256-0.1117-0.01690.0369-0.26280.06650.2713-0.14310.1531-0.0769-0.07280.228-0.04880.24714.276517.32136.7032
20.8640.0286-0.14221.93660.06561.46490.0329-0.05790.0611-0.11280.0689-0.3039-0.15910.2815-0.03640.1285-0.0701-0.00050.1992-0.01390.19761.728816.664228.6853
31.95261.40791.983.84214.21327.8195-0.06610.10920.1788-0.2225-0.23430.4573-0.2657-0.45340.32530.12330.0027-0.03160.217-0.00720.2468-25.718117.514839.2469
43.67971.1734-0.38810.6677-0.09740.33610.3584-0.48260.31190.1871-0.1233-0.0881-0.4470.3176-0.21310.3304-0.1416-0.00010.2843-0.07260.2955-2.009533.247548.0764
53.10831.6064-1.5060.9243-0.71212.06330.15510.3150.44990.01050.15390.2289-0.62170.0691-0.31260.3833-0.0998-0.00270.26880.00450.4088-1.232940.37431.2885
61.39380.0456-0.30481.15070.38461.12780.0558-0.20330.13230.240.0266-0.1631-0.10220.2562-0.03960.1737-0.0623-0.05230.2376-0.02450.1664-4.822819.1647.6134
72.6788-0.29120.49832.603-0.19542.7631-0.17990.0645-0.0572-0.08690.0734-0.08970.038-0.04420.09170.1495-0.06930.01160.0986-0.00090.1235-13.9203-3.905622.8168
81.87660.20320.03811.73150.20391.8808-0.0492-0.0183-0.0522-0.03050.0095-0.01010.1156-0.05960.03070.1237-0.0338-0.02460.13470.0060.1135-13.32642.381830.4248
91.15790.2493-0.36541.94131.22711.931-0.05130.24460.146-0.81590.1602-0.2111-0.46140.1277-0.15640.4629-0.11890.12460.32930.02930.30262.156914.65357.4865
102.35550.5522-2.14661.03050.02153.2948-0.11740.5133-0.0881-0.44810.09150.006-0.0038-0.38560.04460.3557-0.1009-0.00890.2857-0.03480.1994-15.962-8.75929.9012
112.64151.1479-1.68751.8598-0.76133.4243-0.04770.62440.1362-0.51040.16710.20690.0409-0.3664-0.08570.3998-0.0942-0.02780.3526-0.00910.1947-15.4172-4.14583.6012
121.30810.0927-0.31041.56590.04771.6608-0.10.0943-0.2036-0.22140.0971-0.34480.20690.17810.02310.1741-0.01130.04580.1713-0.02350.22410.0364-6.469819.4982
135.3487-1.76441.92813.2341-1.23142.0038-0.1738-0.0676-0.2621-0.07250.197-0.143-0.1040.03510.01030.158-0.08560.03590.1142-0.03980.1455-32.4501-26.906122.4434
142.60320.0113-0.44870.995-0.43181.6524-0.0485-0.0208-0.0967-0.04850.0332-0.1417-0.070.11340.01710.1528-0.05740.01220.1417-0.03650.1611-38.3799-31.172229.6293
151.8603-0.595-0.2480.37280.61663.4347-0.23150.0908-0.9646-0.39790.3865-0.23170.52810.08960.17990.5615-0.2150.2550.2536-0.38890.4934-37.3793-54.220910.9079
160.34710.5907-0.24841.77871.29464.3998-0.15110.1806-0.2967-0.16010.1403-0.5670.17950.5549-0.09670.2383-0.08580.09740.3319-0.07570.3977-21.4161-29.055214.1537
170.82810.2182-0.46381.7119-0.00951.4229-0.21630.2652-0.3083-0.23880.0768-0.41550.13930.1904-0.00390.2474-0.09320.12630.2423-0.10390.3206-26.2255-33.323314.0216
181.3460.5705-0.42931.3505-0.12641.0371-0.22360.4686-0.1045-0.37370.2086-0.07190.0808-0.15830.00550.3128-0.14190.04050.3246-0.06690.1656-40.5534-30.88838.4197
194.56353.27381.81158.59622.31042.69320.0129-0.1264-0.22670.2875-0.00560.27950.28450.1338-0.00770.13360.09290.02360.15750.06060.1532-37.475-0.084374.0778
201.3502-0.2979-0.38781.82450.22611.0396-0.1757-0.2627-0.30970.22330.15180.09580.22920.1614-0.00560.21280.08620.02830.18890.06280.1916-43.59083.65980.8847
213.4992-1.83461.24462.8898-1.27913.06710.0930.329-0.1498-0.4851-0.09120.1810.2997-0.028-0.00550.2474-0.0094-0.05450.1897-0.05750.1827-40.44034.849350.9683
228.5135.5453-3.75397.7169-2.96543.2625-0.57030.5239-0.7433-0.250.51160.64990.7416-0.25590.06880.38540.0770.04460.27040.04380.5751-39.5299-12.52270.7133
232.9543-0.98060.9141.3615-0.41693.48280.22920.2452-0.6055-0.68330.02210.2410.9580.0927-0.25640.4315-0.0065-0.07750.1775-0.07740.3409-41.2586-7.269354.8769
241.6541-0.20890.8431.83060.3713.6313-0.1519-0.1209-0.03860.13580.13920.05280.06770.3303-0.00790.09490.0614-0.00690.18540.01760.1592-36.04245.422774.241
251.3841-0.3207-0.1561.67590.20472.0312-0.0151-0.01510.0246-0.04990.0411-0.0186-0.0470.1722-0.02110.12640.0078-0.0140.1452-0.00420.127-35.489213.117564.0353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 135 )
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 165 )
4X-RAY DIFFRACTION4chain 'A' and (resid 166 through 199 )
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 224 )
6X-RAY DIFFRACTION6chain 'A' and (resid 225 through 391 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 135 )
9X-RAY DIFFRACTION9chain 'B' and (resid 136 through 165 )
10X-RAY DIFFRACTION10chain 'B' and (resid 166 through 210 )
11X-RAY DIFFRACTION11chain 'B' and (resid 211 through 241 )
12X-RAY DIFFRACTION12chain 'B' and (resid 242 through 391 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 25 )
14X-RAY DIFFRACTION14chain 'C' and (resid 26 through 135 )
15X-RAY DIFFRACTION15chain 'C' and (resid 136 through 165 )
16X-RAY DIFFRACTION16chain 'C' and (resid 166 through 210 )
17X-RAY DIFFRACTION17chain 'C' and (resid 211 through 265 )
18X-RAY DIFFRACTION18chain 'C' and (resid 266 through 391 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 25 )
20X-RAY DIFFRACTION20chain 'D' and (resid 26 through 150 )
21X-RAY DIFFRACTION21chain 'D' and (resid 151 through 186 )
22X-RAY DIFFRACTION22chain 'D' and (resid 187 through 210 )
23X-RAY DIFFRACTION23chain 'D' and (resid 211 through 241 )
24X-RAY DIFFRACTION24chain 'D' and (resid 242 through 265 )
25X-RAY DIFFRACTION25chain 'D' and (resid 266 through 391 )

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