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- PDB-2v7b: Crystal structures of a benzoate CoA ligase from Burkholderia xen... -

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Basic information

Entry
Database: PDB / ID: 2v7b
TitleCrystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400
ComponentsBENZOATE-COENZYME A LIGASE
KeywordsLIGASE / BENZOATE OXIDATION / BENZOATE COA LIGASE
Function / homology
Function and homology information


benzoate-CoA ligase / benzoate-CoA ligase activity / secondary metabolite biosynthetic process / ATP binding / membrane
Similarity search - Function
Benzoate-CoA ligase family / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold ...Benzoate-CoA ligase family / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / Benzoate-CoA ligase
Similarity search - Component
Biological speciesBURKHOLDERIA XENOVORANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsJ Boulanger, M. / Bains, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Biochemical and Structural Characterization of the Paralogous Benzoate Coa Ligases from Burkholderia Xenovorans Lb400: Defining the Entry Point Into the Novel Benzoate Oxidation (Box) Pathway.
Authors: Bains, J. / Boulanger, M.J.
History
DepositionJul 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: BENZOATE-COENZYME A LIGASE
B: BENZOATE-COENZYME A LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1434
Polymers114,8992
Non-polymers2442
Water19,1321062
1
A: BENZOATE-COENZYME A LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5722
Polymers57,4491
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BENZOATE-COENZYME A LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5722
Polymers57,4491
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.550, 74.550, 89.900
Angle α, β, γ (deg.)70.06, 79.95, 81.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1545, -0.98799, 0.00246), (-0.98798, 0.15451, 0.00466), (-0.00498, -0.00172, -0.99999)
Vector: 135.19475, 115.50762, 86.72312)

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Components

#1: Protein BENZOATE-COENZYME A LIGASE / BENZOATE COA LIGASE


Mass: 57449.402 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-529
Source method: isolated from a genetically manipulated source
Details: BENZOATE / Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q13WK3, benzoate-CoA ligase
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1062 / 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: 3.82 Å3/Da / Density % sol: 67.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorDate: Apr 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.84→39.41 Å / Num. obs: 141986 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.5
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 3.36 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MDF

1mdf


Resolution: 1.84→36.66 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.726 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 7152 5 %RANDOM
Rwork0.221 ---
obs0.223 134825 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0.12 Å2-0.09 Å2
2--0 Å20.28 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.84→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7520 0 18 1062 8600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.96910478
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46722.822326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.424151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.941558
X-RAY DIFFRACTIONr_chiral_restr0.1020.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025860
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.23787
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25126
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2793
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9671.55020
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44127784
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.43133106
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.674.52694
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: 1.84→1.89 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 500
Rwork0.313 9040

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