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- PDB-6p7u: CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD... -

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Basic information

Entry
Database: PDB / ID: 6p7u
TitleCRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD6) IN COMPLEX WITH INHIBITOR QUIZALOFOP-P FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsProbable propionyl-CoA carboxylase beta chain 6
KeywordsTRANSFERASE / CROTONASE SUPER FAMILY / CARBOXYLTRANSFERASE / TRANSFERASE-HERBICIDE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / acetyl-CoA carboxytransferase / fatty acid elongation, saturated fatty acid / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / peptidoglycan-based cell wall / transferase activity
Similarity search - Function
: / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...: / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-FTJ / Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase beta6 subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.198 Å
AuthorsReddy, M.C.M. / Sacchettini, J.C. / Center for Structural Genomics of Infectious Diseases (CSGID)
Citation
Journal: To Be Published
Title: Inhibition of Mycobacterium tuberculosis acetyl-CoA carboxyltransferase(AccD6)d omain of acetyl-coenzyme A carboxylase by quizalofop-p
Authors: Reddy, M.C.M. / Sacchettini, J.C.
#1: Journal: Antimicrob.Agents Chemother. / Year: 2014
Title: Structure, Activity, and Inhibition of the Carboxyltransferase beta-Subunit of Acetyl Coenzyme A Carboxylase (AccD6) from Mycobacterium tuberculosis
Authors: Reddy, M.C.M. / Sacchettini, J.C.
History
DepositionJun 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: Probable propionyl-CoA carboxylase beta chain 6
B: Probable propionyl-CoA carboxylase beta chain 6
C: Probable propionyl-CoA carboxylase beta chain 6
D: Probable propionyl-CoA carboxylase beta chain 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,1758
Polymers200,7964
Non-polymers1,3794
Water14,286793
1
A: Probable propionyl-CoA carboxylase beta chain 6
B: Probable propionyl-CoA carboxylase beta chain 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0874
Polymers100,3982
Non-polymers6892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-40 kcal/mol
Surface area31750 Å2
MethodPISA
2
C: Probable propionyl-CoA carboxylase beta chain 6
D: Probable propionyl-CoA carboxylase beta chain 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0874
Polymers100,3982
Non-polymers6892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-41 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.604, 153.343, 102.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Probable propionyl-CoA carboxylase beta chain 6 / PCCase / Propanoyl-CoA:carbon dioxide ligase


Mass: 50198.934 Da / Num. of mol.: 4 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: accD6, Rv2247, MTCY427.28 / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WQH5, propionyl-CoA carboxylase
#2: Chemical
ChemComp-FTJ / (2R)-2-{4-[(6-chloroquinoxalin-2-yl)oxy]phenoxy}propanoic acid


Mass: 344.749 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H13ClN2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / 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: 2.3 Å3/Da / Density meas: 1.35 Mg/m3 / Density % sol: 47 %
Description: Thick, triangular, and plate-like with sharp edges
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Li2SO4, 0.1 M Tris pH 7, 1 M potassium sodium tartrate
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) LIQUID N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.198→48.762 Å / Num. obs: 117732 / % possible obs: 97.49 % / Redundancy: 7 % / Net I/σ(I): 1.34
Reflection shellResolution: 2.198→2.432 Å / Num. unique obs: 117732

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G2R

4g2r


Resolution: 2.198→48.762 Å / FOM work R set: 0.8533 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 5914 5.02 %
Rwork0.1707 111818 -
obs0.1725 117732 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.21 Å2 / Biso mean: 33.52 Å2 / Biso min: 5.13 Å2
Refinement stepCycle: final / Resolution: 2.198→48.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12323 0 96 793 13212
Biso mean--29.44 37.42 -
Num. residues----1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812692
X-RAY DIFFRACTIONf_angle_d1.10817280
X-RAY DIFFRACTIONf_chiral_restr0.0741978
X-RAY DIFFRACTIONf_plane_restr0.0052288
X-RAY DIFFRACTIONf_dihedral_angle_d15.2314448
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 (%)
2.1977-2.22270.28731460.21022626277270
2.2227-2.24890.26381790.21813091327083
2.2489-2.27630.26711580.22193366352488
2.2763-2.30510.25361970.20433490368793
2.3051-2.33540.28291720.20693666383896
2.3354-2.36740.26951960.20213686388298
2.3674-2.40120.25341910.19523786397799
2.4012-2.43710.24782020.19623735393799
2.4371-2.47520.22561980.197138144012100
2.4752-2.51570.26651990.191337693968100
2.5157-2.55910.22651930.193738003993100
2.5591-2.60560.28211910.196638073998100
2.6056-2.65580.25352100.195337473957100
2.6558-2.710.24751930.188938634056100
2.71-2.76890.23661910.189137693960100
2.7689-2.83330.23551970.196838134010100
2.8333-2.90410.25582040.203937913995100
2.9041-2.98260.25931920.195838364028100
2.9826-3.07040.2182010.198738184019100
3.0704-3.16950.2141950.186638054000100
3.1695-3.28270.2242210.181837783999100
3.2827-3.41410.2121990.16738634062100
3.4141-3.56950.19032050.159938294034100
3.5695-3.75760.19171830.147138514034100
3.7576-3.99290.1861890.139838494038100
3.9929-4.30110.15592420.134738274069100
4.3011-4.73360.1512210.125538414062100
4.7336-5.41780.16681880.144339244112100
5.4178-6.82280.21092140.170939204134100
6.8228-48.77380.15652470.16514058430599
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)
10.04790.05760.03820.08590.00780.075-0.0840.0989-0.0332-0.09220.04150.19810.1476-0.3508-0.0456-0.0385-0.3448-0.06780.2554-0.03020.206-73.56920.068-44.1222
20.1067-0.05580.08140.0315-0.04280.0617-0.0103-0.0652-0.07130.04480.10530.07570.1139-0.16290.0090.2092-0.0910.05830.21380.00660.2473-67.49120.4816-26.4495
30.2666-0.17330.0730.16450.00540.0836-0.0545-0.0876-0.07650.10350.06290.09010.0759-0.0810.00040.2301-0.05410.07640.09770.03010.1409-55.047317.695-13.0801
40.1064-0.00970.06020.08480.0080.1565-0.0722-0.0285-0.05640.0352-0.0074-0.00020.1272-0.0567-0.04870.1139-0.0180.04870.0280.03040.0972-45.837823.7946-22.3566
50.00640.00390.00710.00280.00220.01110.0131-0.0137-0.0710.10670.0073-0.0631-0.04240.007300.4357-0.0257-0.11420.39820.02150.4884-20.312314.5345-5.0178
60.0179-0.0076-0.01060.0464-0.01540.0150.0216-0.01340.07620.1561-0.0266-0.0389-0.1199-0.02-0.00150.1832-0.02510.04660.1681-0.01530.1504-48.202335.1024-11.6213
70.0558-0.0353-0.13420.10490.14680.4276-0.0625-0.00270.04410.0270.0394-0.0424-0.04870.4272-0.00440.0868-0.0306-0.01250.19840.03890.1352-25.945232.685-37.4702
80.1978-0.02420.1210.0054-0.01390.0775-0.04570.1657-0.0594-0.1569-0.0342-0.04090.14920.1001-0.00620.2165-0.0270.01380.13890.02690.1449-40.007220.4609-59.3964
90.1603-0.0193-0.0140.0138-0.01290.0562-0.15560.026-0.0955-0.0149-0.00360.02290.1563-0.091-0.08550.2604-0.16210.03990.1492-0.01230.1706-56.551511.9031-58.2845
100.0115-0.0261-0.00050.0650.00130.0667-0.03790.06480.0113-0.0981-0.00260.09080.0651-0.1146-0.04150.2411-0.1132-0.07960.32170.03690.1503-53.673424.7268-68.3787
110.1687-0.0909-0.06190.12080.12990.1457-0.10320.1632-0.15680.0296-0.0775-0.06760.20050.344-0.13690.11640.120.03790.36410.03520.15930.7937-33.5364-17.2398
120.0064-0.0172-0.00710.13220.0810.048-0.0037-0.035-0.00270.144-0.0177-0.02920.02830.20820.00430.12660.00610.00290.2710.03860.1379-3.9503-24.4702-3.8473
130.01280.01150.00070.012-0.00150.011-0.0872-0.08330.20630.0737-0.0399-0.0468-0.06470.0848-0.00010.3369-0.0513-0.0420.26770.01710.2238-9.9539-10.7410.2384
140.0320.0024-0.00440.00690.010.0134-0.04470.00540.08230.0276-0.0542-0.0846-0.02780.0941-00.196-0.0253-0.00610.14370.04510.1666-15.2653-15.15990.7907
150.1018-0.03420.01030.0155-0.00130.002-0.1927-0.00940.16360.11220.12320.0326-0.17620.0556-0.00340.2495-0.005-0.0020.1316-0.00560.1756-24.8666-11.06393.1019
160.0398-0.01210.02770.0518-0.01140.0238-0.0545-0.07360.04310.0103-0.02070.0538-0.0552-0.0457-0.08280.39460.1420.05380.3157-0.11310.2263-33.83420.580314.6151
170.0016-0.00310.00260.0086-0.00670.0056-0.0938-0.0712-0.08770.0227-0.00550.05330.0222-0.01060.00010.35730.02640.05780.30730.01310.1465-21.3965-24.562314.4595
180.0774-0.0585-0.03260.04610.02460.1086-0.031-0.0166-0.01870.141-0.00520.22860.0383-0.15960.00060.14870.01960.04630.0943-0.00940.2289-45.7978-10.3949-8.6053
190.05670.00730.01360.0172-0.02450.04850.02940.08660.0525-0.0224-0.00260.0312-0.046-0.05870.00820.17270.0367-0.01880.0878-0.01210.2136-40.0404-11.6215-26.1564
200.02520.0243-0.00730.029-0.01350.01690.0590.15450.091-0.0693-0.07260.0591-0.07210.02090.00230.26940.0717-0.03370.22490.06290.2178-27.4781-12.5184-39.5213
210.0112-0.01570.00170.02120.00130.0173-0.00060.02120.0242-0.0346-0.05590.00630.03140.066-00.13210.0204-0.02070.13320.00410.1629-25.6917-16.0792-28.5691
220.0466-0.04910.01070.056-0.01490.03020.03980.14260.0878-0.0009-0.0036-0.1038-0.11860.16030.00020.14030.0284-0.00150.21260.00610.1658-15.1237-20.8901-31.1329
230.00310.0014-0.0010.00210.00190.0043-0.04310.00320.0428-0.0287-0.0366-0.0182-0.0189-0.0198-0.00010.64310.0750.13590.88270.07070.70948.8404-14.6116-46.5181
240.0007-0.0004-0.00060.00820.00420.00180.0630.1015-0.026-0.0694-0.008-0.04980.0720.10670.02820.24920.1174-0.01980.2857-0.05150.1191-21.8248-30.3732-40.2278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 145 )A13 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 226 )A146 - 226
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 268 )A227 - 268
4X-RAY DIFFRACTION4chain 'A' and (resid 269 through 401 )A269 - 401
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 428 )A402 - 428
6X-RAY DIFFRACTION6chain 'A' and (resid 429 through 466 )A429 - 466
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 213 )B13 - 213
8X-RAY DIFFRACTION8chain 'B' and (resid 214 through 312 )B214 - 312
9X-RAY DIFFRACTION9chain 'B' and (resid 313 through 425 )B313 - 425
10X-RAY DIFFRACTION10chain 'B' and (resid 426 through 466 )B426 - 466
11X-RAY DIFFRACTION11chain 'C' and (resid 13 through 121 )C13 - 121
12X-RAY DIFFRACTION12chain 'C' and (resid 122 through 226 )C122 - 226
13X-RAY DIFFRACTION13chain 'C' and (resid 227 through 268 )C227 - 268
14X-RAY DIFFRACTION14chain 'C' and (resid 269 through 313 )C269 - 313
15X-RAY DIFFRACTION15chain 'C' and (resid 314 through 393 )C314 - 393
16X-RAY DIFFRACTION16chain 'C' and (resid 394 through 446 )C394 - 446
17X-RAY DIFFRACTION17chain 'C' and (resid 447 through 466 )C447 - 466
18X-RAY DIFFRACTION18chain 'D' and (resid 13 through 145 )D13 - 145
19X-RAY DIFFRACTION19chain 'D' and (resid 146 through 226 )D146 - 226
20X-RAY DIFFRACTION20chain 'D' and (resid 227 through 268 )D227 - 268
21X-RAY DIFFRACTION21chain 'D' and (resid 269 through 313 )D269 - 313
22X-RAY DIFFRACTION22chain 'D' and (resid 314 through 401 )D314 - 401
23X-RAY DIFFRACTION23chain 'D' and (resid 402 through 426 )D402 - 426
24X-RAY DIFFRACTION24chain 'D' and (resid 427 through 466 )D427 - 466

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