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- PDB-2a7s: Crystal Structure of the Acyl-CoA Carboxylase, AccD5, from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 2a7s
TitleCrystal Structure of the Acyl-CoA Carboxylase, AccD5, from Mycobacterium tuberculosis
ComponentsProbable propionyl-CoA carboxylase beta chain 5
KeywordsLIGASE / carboxylase / carboxyltransferase / acetyl-CoA carboxylase / propionyl-CoA carboxylase / Acyl-CoA Carboxylase / mycolic acid / fatty acid / polyketide
Function / homology
Function and homology information


acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / carbon fixation / cell wall / peptidoglycan-based cell wall / lipid metabolic process / transferase activity ...acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / carbon fixation / cell wall / peptidoglycan-based cell wall / lipid metabolic process / transferase activity / protein-containing complex / identical protein binding / plasma membrane
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 beta5 subunit / Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase beta5 subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLin, T. / Melgar, M. / Purdon, J. / Tseng, T. / Tsai, S.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis.
Authors: Lin, T.W. / Melgar, M.M. / Kurth, D. / Swamidass, S.J. / Purdon, J. / Tseng, T. / Gago, G. / Baldi, P. / Gramajo, H. / Tsai, S.C.
History
DepositionJul 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable propionyl-CoA carboxylase beta chain 5
B: Probable propionyl-CoA carboxylase beta chain 5
C: Probable propionyl-CoA carboxylase beta chain 5
D: Probable propionyl-CoA carboxylase beta chain 5
E: Probable propionyl-CoA carboxylase beta chain 5
F: Probable propionyl-CoA carboxylase beta chain 5


Theoretical massNumber of molelcules
Total (without water)356,5206
Polymers356,5206
Non-polymers00
Water20,4651136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45530 Å2
ΔGint-242 kcal/mol
Surface area101220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.252, 175.252, 342.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a hexamer in the asymmetric unit (chain A-F)

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Components

#1: Protein
Probable propionyl-CoA carboxylase beta chain 5 / PCCase / Propanoyl-CoA:carbon dioxide ligase


Mass: 59419.969 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: accD5, pccB / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P96885, UniProt: P9WQH7*PLUS, propionyl-CoA carboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1136 / 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: 3.35 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 0.1 M sodium citrate pH 5.6, 0.2 M ammonium acetate, 15% PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2004 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 118668 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.107 / Net I/σ(I): 7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.429 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ACYL-COA CARBOXYLASE FROM STREPTOMYCES COELICOLOR, PCCB

Resolution: 2.9→47.88 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 26374.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 10861 10 %RANDOM
Rwork0.193 ---
obs0.193 108530 91.5 %-
all-118237 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.9355 Å2 / ksol: 0.293853 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å20 Å2
2---1.74 Å20 Å2
3---3.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24180 0 0 1136 25316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d2.462
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 1676 10 %
Rwork0.284 15154 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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