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- PDB-2bzr: Crystal structure of accD5 (Rv3280), an acyl-CoA carboxylase beta... -

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Basic information

Entry
Database: PDB / ID: 2bzr
TitleCrystal structure of accD5 (Rv3280), an acyl-CoA carboxylase beta- subunit from Mycobacterium tuberculosis
ComponentsPROPIONYL-COA CARBOXYLASE BETA CHAIN 5
KeywordsTRANSFERASE / MYCOBACTERIUM TUBERCULOSIS / FATTY ACID BIOSYNTHESIS / ACCASE / LIGASE / MYCOBACTERIUM TUBERCULOSIS STRUCTURAL PROTEOMICS PROJECT / XMTB / STRUCTURAL GENOMICS
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / acetyl-CoA carboxytransferase / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / cell wall / acetyl-CoA carboxylase activity / carbon fixation / peptidoglycan-based cell wall / lipid metabolic process / transferase activity ...Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / acetyl-CoA carboxytransferase / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / cell wall / acetyl-CoA carboxylase activity / carbon fixation / 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 ...: / 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: 2.2 Å
AuthorsHolton, S.J.
CitationJournal: FEBS Lett. / Year: 2006
Title: Structural Diversity in the Six-Fold Redundant Set of Acyl-Coa Carboxyltransferases in Mycobacterium Tuberculosis.
Authors: Holton, S.J. / King-Scott, S. / Eddine, A.N. / Kaufmann, S.H. / Wilmanns, M.
History
DepositionAug 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROPIONYL-COA CARBOXYLASE BETA CHAIN 5
B: PROPIONYL-COA CARBOXYLASE BETA CHAIN 5
C: PROPIONYL-COA CARBOXYLASE BETA CHAIN 5
D: PROPIONYL-COA CARBOXYLASE BETA CHAIN 5
E: PROPIONYL-COA CARBOXYLASE BETA CHAIN 5
F: PROPIONYL-COA CARBOXYLASE BETA CHAIN 5


Theoretical massNumber of molelcules
Total (without water)356,1726
Polymers356,1726
Non-polymers00
Water30,4451690
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)173.562, 173.562, 339.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2159-

HOH

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Components

#1: Protein
PROPIONYL-COA CARBOXYLASE BETA CHAIN 5 / ACYL-COA CARBOXYTRANSFERASE / PCCASE / PROPANOYL-COA CARBON DIOXIDE LIGASE


Mass: 59361.938 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P96885, UniProt: P9WQH7*PLUS, propionyl-CoA carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1690 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHAS A CATALYTIC ACTIVITY

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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: 3.66 Å3/Da / Density % sol: 66.15 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97889
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2.2→32.22 Å / Num. obs: 251643 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.79 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.27
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.95 / % possible all: 78.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.09 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.984 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 13260 5.32 %THIN RESOLUTION SHELLS
Rwork0.176 ---
obs0.178 251516 100 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.421 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23178 0 0 1690 24868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02223748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.96832248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91953051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56624.0861067
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.303153881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.02215165
X-RAY DIFFRACTIONr_chiral_restr0.150.23642
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218201
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.211740
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.216201
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.21943
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9821.515619
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.567224276
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.75139213
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2434.57965
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 9.43→32.09 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.203 153
Rwork0.199 3349

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