[English] 日本語
Yorodumi
- PDB-8ecm: Crystal Structure Analysis of Acetyl-CoA acetyltransferase from F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ecm
TitleCrystal Structure Analysis of Acetyl-CoA acetyltransferase from Firmicutes bacterium
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / Acetyl-CoA acetyltransferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesFirmicutes bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsSeo, H.S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Med / Year: 2023
Title: Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease.
Authors: Mehta, R.S. / Mayers, J.R. / Zhang, Y. / Bhosle, A. / Glasser, N.R. / Nguyen, L.H. / Ma, W. / Bae, S. / Branck, T. / Song, K. / Sebastian, L. / Pacheco, J.A. / Seo, H.S. / Clish, C. / Dhe- ...Authors: Mehta, R.S. / Mayers, J.R. / Zhang, Y. / Bhosle, A. / Glasser, N.R. / Nguyen, L.H. / Ma, W. / Bae, S. / Branck, T. / Song, K. / Sebastian, L. / Pacheco, J.A. / Seo, H.S. / Clish, C. / Dhe-Paganon, S. / Ananthakrishnan, A.N. / Franzosa, E.A. / Balskus, E.P. / Chan, A.T. / Huttenhower, C.
History
DepositionSep 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
E: Acetyl-CoA acetyltransferase
F: Acetyl-CoA acetyltransferase
G: Acetyl-CoA acetyltransferase
H: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)359,9008
Polymers359,9008
Non-polymers00
Water21,4921193
1
A: Acetyl-CoA acetyltransferase


  • defined by author
  • Evidence: gel filtration
  • 45 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,9881
Polymers44,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl-CoA acetyltransferase


  • defined by author
  • 45 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,9881
Polymers44,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetyl-CoA acetyltransferase


  • defined by author
  • 45 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,9881
Polymers44,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acetyl-CoA acetyltransferase


  • defined by author
  • 45 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,9881
Polymers44,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Acetyl-CoA acetyltransferase


  • defined by author
  • 45 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,9881
Polymers44,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Acetyl-CoA acetyltransferase


  • defined by author
  • 45 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,9881
Polymers44,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Acetyl-CoA acetyltransferase


  • defined by author
  • 45 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,9881
Polymers44,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Acetyl-CoA acetyltransferase


  • defined by author
  • 45 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)44,9881
Polymers44,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.230, 81.460, 160.190
Angle α, β, γ (deg.)95.610, 100.450, 108.270
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Acetyl-CoA acetyltransferase


Mass: 44987.523 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Firmicutes bacterium (bacteria) / Gene: BN516_00284 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R6CZ24
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 100 mM sodium acetate, pH 4.9, 55% MPD, 20 mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→76.29 Å / Num. obs: 263888 / % possible obs: 94.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 39.07 Å2 / Rpim(I) all: 0.07 / Rrim(I) all: 0.099 / Net I/σ(I): 7.1 / Num. measured all: 500388
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.89-1.920.725354131561.1681.65193.8
5.13-76.3520.425094135490.0520.07396.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
xia23.9.0data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XL2
Resolution: 1.89→73.46 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 13239 5.02 %
Rwork0.1757 250468 -
obs0.1774 263707 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.73 Å2 / Biso mean: 50.4955 Å2 / Biso min: 26.79 Å2
Refinement stepCycle: final / Resolution: 1.89→73.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24521 0 0 1193 25714
Biso mean---48.76 -
Num. residues----3364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.910.4414410.48292873393
1.91-1.930.384450.36948386883194
1.93-1.960.36794480.34468319876794
1.96-1.980.35684440.32568324876894
1.98-2.010.34314350.31168223865893
2.01-2.040.32684470.29818370881794
2.04-2.070.31413980.27898232863093
2.07-2.10.30174340.25848352878693
2.1-2.130.28714220.24578285870793
2.13-2.160.28424620.23918205866793
2.16-2.20.27684670.22828240870792
2.2-2.240.26154190.21548076849591
2.24-2.280.24544280.20537784821288
2.28-2.330.23614500.19947862831289
2.33-2.380.23394370.1968489892696
2.38-2.440.25674640.19818540900496
2.44-2.50.24574250.19468553897896
2.5-2.570.24454690.18448421889096
2.57-2.640.21654650.17828464892996
2.64-2.730.24014300.18198488891895
2.73-2.820.22344240.17398519894395
2.82-2.940.21254170.17168410882795
2.94-3.070.22164030.18168406880994
3.07-3.230.2214510.17198156860792
3.23-3.430.19134160.15948198861491
3.43-3.70.18414690.14898555902497
3.7-4.070.16184100.13758639904997
4.07-4.660.1454780.12638567904597
4.66-5.870.1844830.15978546902996
5.87-73.460.18744580.16738567902597
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)
11.3856-0.5-0.03191.5474-0.1290.9324-0.05290.04-0.15040.0583-0.0350.25180.0621-0.2906-0.00010.4819-0.02360.00770.4416-0.01490.4318-40.6751-8.46615.142
20.22960.0650.16520.3950.26511.2381-0.08920.140.0755-0.12640.05780.0544-0.2762-0.0731-00.5408-0.00580.00010.39090.01240.3973-28.24554.29037.7171
31.75870.6511-0.25922.60811.10511.95910.03940.15760.383-0.4201-0.16390.3692-0.6045-0.3772-0.01870.6660.1087-0.1220.49670.03070.5422-43.55799.43374.4253
40.3864-0.0821-0.15151.1980.48141.0371-0.06730.38380.1476-0.5285-0.08160.4528-0.4053-0.3104-0.00040.70230.0593-0.14880.61880.00750.5707-45.46893.2627-3.2129
50.67550.20310.24920.8777-0.06830.6963-0.1360.2737-0.113-0.17540.1978-0.2375-0.13640.162200.54-0.08450.0580.4569-0.04920.4448-19.0375-8.17010.2371
60.51880.29080.47360.44060.07780.45420.02390.0084-0.29850.3081-0.14580.2306-0.164-0.1647-0.00080.5187-0.04840.0190.28670.01340.4086-22.97346.809627.0773
71.07010.83020.59171.71550.73631.59540.15280.0525-0.43390.32380.1023-0.56020.2190.19460.0010.55410.0398-0.14260.3813-0.03310.6863-10.6994-18.493521.838
80.55610.32010.23210.6751-0.14250.2494-0.03320.2883-0.257-0.13870.1668-0.16420.02720.113900.5679-0.09640.04820.4788-0.07250.4468-20.6538-19.0375-3.8497
90.9740.43330.24871.220.02690.86180.09250.2188-0.30880.05230.1483-0.45350.2380.23050.00010.52990.0252-0.05060.4209-0.08670.6266-16.0773-26.02949.4568
101.1092-0.2287-0.51140.8685-0.06271.2157-0.0511-0.1190.278-0.0256-0.10830.1042-0.1281-0.1388-0.00070.47730.0428-0.07020.34910.00260.3829-19.935139.165642.6013
110.7440.26080.4040.19320.76991.04410.071-0.1609-0.15780.1136-0.10640.03240.1925-0.206300.478-0.0106-0.02380.35570.07180.3438-15.533323.799844.7561
121.8812-0.05350.24521.31010.22360.6742-0.0823-0.27820.2555-0.1758-0.0750.40620.0781-0.87510.00010.5498-0.0515-0.03140.6321-0.1120.5109-37.354931.560947.1431
131.97990.67250.59261.31270.57031.29060.1675-0.6236-0.04680.1298-0.29690.1950.2492-0.3614-0.00540.4889-0.08560.02510.60370.00740.3396-25.323428.55759.0851
141.68380.13450.07280.7152-0.4451.2294-0.0407-0.1119-0.3250.14080.0534-0.18620.13790.09760.00020.50530.0612-0.07920.33350.10160.42162.713920.837548.8377
151.01830.43390.37960.90490.41470.725-0.00850.0468-0.1513-0.06480.0598-0.18960.04240.0838-0.00010.46120.03090.01140.28970.04220.3675-2.158326.925235.3532
161.35510.03990.43761.26210.60521.67480.01530.1216-0.0869-0.16920.1189-0.308-0.00820.18840.00040.469-0.00940.020.36530.02030.41977.977730.431834.4934
171.32850.0375-0.66611.8390.56540.9657-0.068-0.085-0.14770.17610.2854-0.32380.02360.3590.00020.4749-0.0006-0.00990.41510.00160.427314.334234.419340.4225
181.8547-0.5321-0.1410.9611-0.07040.7199-0.02070.59740.4169-0.2043-0.0499-0.0444-0.0618-0.0143-0.00230.36680.02580.02960.51020.16080.3528-32.1049-8.979570.7538
191.14850.1963-0.20190.99910.29350.1005-0.00690.05710.04830.0473-0.0401-0.0313-0.03850.088600.32360.03610.00180.36510.0470.3209-33.328-16.701488.3482
202.3873-0.05950.33750.82830.47011.57430.02950.237-0.13640.01790.0081-0.15110.03220.1979-0.00030.32130.05780.00830.42550.02330.3552-20.7715-24.571879.6019
211.1419-0.55670.35631.27070.20020.21250.11940.7979-0.2268-0.50180.0221-0.0907-0.1670.01690.00160.44980.00260.03230.6526-0.05570.4009-25.7845-28.571468.2877
221.80960.0060.43381.6894-0.79210.472-0.0996-0.0364-0.0404-0.0675-0.00120.1652-0.0264-0.0104-0.00020.3362-0.00680.06610.43720.01040.3999-55.2975-20.341589.2199
231.5980.33410.2782-0.01880.25770.58920.02430.04810.2471-0-0.08950.1827-0.0803-0.020500.34140.03890.0010.38010.04250.355-44.3204-10.525484.6336
242.4529-0.140.44992.29720.42520.8930.0295-0.3450.45460.1676-0.260.3848-0.2297-0.35850.00030.41350.07490.05030.5792-0.1040.6077-63.8265-2.357491.117
252.3244-0.00790.31311.32980.36381.33950.01370.24940.3861-0.1434-0.17080.3082-0.182-0.1256-0.00030.37530.0807-0.04720.50510.02490.5058-60.0245-8.2875.3929
260.7366-0.80340.35530.854-0.10730.88710.32150.1302-0.32750.2336-0.29220.33340.3015-0.4324-0.00010.4815-0.0117-0.03190.6336-0.03330.5312-63.9-17.933274.2826
271.17140.76320.80871.09990.48370.93210.1887-0.21180.22710.2836-0.23740.10360.1923-0.0943-0.00020.488-0.03970.06760.4239-0.04040.4377-16.960614.8891118.8797
282.06510.30450.68621.32830.29671.9257-0.05210.38330.3505-0.1418-0.00840.0908-0.07840.1344-00.3937-0.01630.020.50310.05360.5352-13.466526.195299.0502
290.50540.4354-0.16690.90130.13580.33090.2328-0.26230.33370.1722-0.23350.19120.0416-0.0108-0.00010.4692-0.09250.04980.4581-0.05930.4583-8.251226.5691125.9866
300.76960.3871-0.07391.2078-0.22691.0905-0.0669-0.03740.45310.1666-0.0630.1529-0.14650.1572-0.00010.3801-0.016-0.00150.42570.0210.5874-8.625133.3066111.9035
310.506-0.4592-0.05740.9725-0.65070.789-0.0466-0.46650.39860.2985-0.29610.49990.0786-0.5375-0.0010.5049-0.08690.13750.8213-0.31380.8004-41.903223.9098123.6168
321.62390.70530.91160.88490.75361.57890.2613-0.490.28540.4961-0.50260.28410.3648-0.5728-0.19720.59-0.21790.15390.6501-0.11170.4846-32.351313.0745122.6245
331.0093-0.5743-0.36053.7112-0.19081.09340.3364-0.72180.12270.0933-0.30110.63350.6317-0.87360.03320.8123-0.49040.22321.1036-0.24270.8323-48.00187.6366125.8361
341.71660.5670.48050.6220.44191.2580.2222-0.78360.11420.5396-0.45140.27360.5904-0.7239-0.09440.9329-0.40530.23591.0129-0.20910.5891-34.766213.7004138.1542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 81 )A3 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 173 )A82 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 311 )A174 - 311
4X-RAY DIFFRACTION4chain 'A' and (resid 312 through 421 )A312 - 421
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 119 )B2 - 119
6X-RAY DIFFRACTION6chain 'B' and (resid 120 through 143 )B120 - 143
7X-RAY DIFFRACTION7chain 'B' and (resid 144 through 277 )B144 - 277
8X-RAY DIFFRACTION8chain 'B' and (resid 278 through 311 )B278 - 311
9X-RAY DIFFRACTION9chain 'B' and (resid 312 through 421 )B312 - 421
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 66 )C2 - 66
11X-RAY DIFFRACTION11chain 'C' and (resid 67 through 173 )C67 - 173
12X-RAY DIFFRACTION12chain 'C' and (resid 174 through 215 )C174 - 215
13X-RAY DIFFRACTION13chain 'C' and (resid 216 through 422 )C216 - 422
14X-RAY DIFFRACTION14chain 'D' and (resid 3 through 66 )D3 - 66
15X-RAY DIFFRACTION15chain 'D' and (resid 67 through 193 )D67 - 193
16X-RAY DIFFRACTION16chain 'D' and (resid 194 through 330 )D194 - 330
17X-RAY DIFFRACTION17chain 'D' and (resid 331 through 425 )D331 - 425
18X-RAY DIFFRACTION18chain 'E' and (resid 3 through 81 )E3 - 81
19X-RAY DIFFRACTION19chain 'E' and (resid 82 through 173 )E82 - 173
20X-RAY DIFFRACTION20chain 'E' and (resid 174 through 394 )E174 - 394
21X-RAY DIFFRACTION21chain 'E' and (resid 395 through 423 )E395 - 423
22X-RAY DIFFRACTION22chain 'F' and (resid 2 through 43 )F2 - 43
23X-RAY DIFFRACTION23chain 'F' and (resid 44 through 173 )F44 - 173
24X-RAY DIFFRACTION24chain 'F' and (resid 174 through 245 )F174 - 245
25X-RAY DIFFRACTION25chain 'F' and (resid 246 through 394 )F246 - 394
26X-RAY DIFFRACTION26chain 'F' and (resid 395 through 424 )F395 - 424
27X-RAY DIFFRACTION27chain 'G' and (resid 2 through 143 )G2 - 143
28X-RAY DIFFRACTION28chain 'G' and (resid 144 through 277 )G144 - 277
29X-RAY DIFFRACTION29chain 'G' and (resid 278 through 311 )G278 - 311
30X-RAY DIFFRACTION30chain 'G' and (resid 312 through 421 )G312 - 421
31X-RAY DIFFRACTION31chain 'H' and (resid 4 through 43 )H4 - 43
32X-RAY DIFFRACTION32chain 'H' and (resid 44 through 193 )H44 - 193
33X-RAY DIFFRACTION33chain 'H' and (resid 194 through 245 )H194 - 245
34X-RAY DIFFRACTION34chain 'H' and (resid 246 through 420 )H246 - 420

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more