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- PDB-4l6w: Carboxyltransferase subunit (AccD6) of Mycobacterium tuberculosis... -

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Basic information

Entry
Database: PDB / ID: 4l6w
TitleCarboxyltransferase subunit (AccD6) of Mycobacterium tuberculosis acetyl-CoA carboxylase
ComponentsProbable propionyl-CoA carboxylase beta chain 6
KeywordsLIGASE / Crotonase fold / CoA binding
Function / homology
Function and homology information


acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / propionyl-CoA carboxylase activity / fatty acid elongation, saturated fatty acid / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / ligase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase beta6 subunit / Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase beta6 subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAnandhakrishnan, M. / Ehebauer, M.T. / Wilmanns, M.
CitationJournal: To be Published
Title: Structural analysis of the carboxyltransferase subunit of Mycobacterium tuberculosis acetyl-CoA carboxylase
Authors: Anandhakrishnan, M. / Ehebauer, M.T. / Wilmanns, M.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)104,7412
Polymers104,7412
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-50 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.942, 90.311, 154.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 150
2114B1 - 150
1126A151 - 190
2126B151 - 190
1134A191 - 215
2134B191 - 215
1144A216 - 395
2144B216 - 395
1156A396 - 430
2156B396 - 430
1164A431 - 460
2164B431 - 460

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.188521, 0.367309, -0.910793), (0.368966, -0.88597, -0.280928), (-0.910123, -0.283091, -0.302549)20.3316, 30.86143, 38.84181

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Components

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


Mass: 52370.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: accD6, MT2307, MTCY427.28, Rv2247 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P63407, UniProt: P9WQH5*PLUS, acetyl-CoA carboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 27% (w/v) PEG 3350, 0.3 M ammonium sulphate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2395 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2012 / Details: 25 Hz, 450 micron sensor thickness
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2395 Å / Relative weight: 1
ReflectionResolution: 1.947→76.942 Å / Num. all: 79503 / Num. obs: 79385 / % possible obs: 99.85 % / Observed criterion σ(I): -3 / Redundancy: 12.88 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 34.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.14 / Num. unique all: 12489 / % possible all: 98.59

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BZR

2bzr


Resolution: 1.95→68.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.337 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24356 3977 5 %RANDOM
Rwork0.17383 ---
all0.17721 75286 --
obs0.17721 75286 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.222 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0 Å2
2--0.35 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.95→68.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 0 195 6336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196257
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9528504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00522.835261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61815946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7051556
X-RAY DIFFRACTIONr_chiral_restr0.130.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214789
X-RAY DIFFRACTIONr_rigid_bond_restr7.44436257
X-RAY DIFFRACTIONr_sphericity_free23.818559
X-RAY DIFFRACTIONr_sphericity_bonded26.70456278
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1985MEDIUM POSITIONAL0.340.5
1985MEDIUM THERMAL10.662
243LOOSE POSITIONAL0.415
243LOOSE THERMAL14.5610
3201MEDIUM POSITIONAL0.240.5
3201MEDIUM THERMAL8.432
41276MEDIUM POSITIONAL0.620.5
41276MEDIUM THERMAL9.232
521LOOSE POSITIONAL0.195
521LOOSE THERMAL16.2110
6220MEDIUM POSITIONAL0.420.5
6220MEDIUM THERMAL12.412
LS refinement shellResolution: 1.947→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 288 -
Rwork0.192 5305 -
obs--96.76 %

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