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- PDB-4rmn: Crystal structure of a benzoate coenzyme A ligase with 2-Thiophen... -

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Basic information

Entry
Database: PDB / ID: 4rmn
TitleCrystal structure of a benzoate coenzyme A ligase with 2-Thiophene Carboxylic acid
ComponentsBenzoate-coenzyme A ligase
KeywordsLIGASE / Substrate Specificity / Kinetics
Function / homology
Function and homology information


benzoate-CoA ligase / benzoate-CoA ligase activity / acid-thiol ligase activity / CoA-ligase activity / secondary metabolite biosynthetic process / ATP binding
Similarity search - Function
Rossmann fold - #12820 / Benzoate-CoA ligase family / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme ...Rossmann fold - #12820 / Benzoate-CoA ligase family / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
THIOPHENE-2-CARBOXYLIC ACID / Benzoate-CoA ligase / Benzoate-coenzyme A ligase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsStrom, S. / Nosrati, M. / Thornburg, C. / Walker, K.D. / Geiger, J.H.
CitationJournal: Biochemistry / Year: 2015
Title: Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity.
Authors: Thornburg, C.K. / Wortas-Strom, S. / Nosrati, M. / Geiger, J.H. / Walker, K.D.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)114,74213
Polymers113,5842
Non-polymers1,15711
Water10,305572
1
B: Benzoate-coenzyme A ligase
hetero molecules

A: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,74213
Polymers113,5842
Non-polymers1,15711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area6110 Å2
ΔGint3 kcal/mol
Surface area37400 Å2
MethodPISA
2
A: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1414
Polymers56,7921
Non-polymers3483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Benzoate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6019
Polymers56,7921
Non-polymers8098
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.644, 94.609, 95.701
Angle α, β, γ (deg.)90.00, 104.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Benzoate-coenzyme A ligase


Mass: 56792.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: badA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q93TK0, UniProt: Q6NC13*PLUS
#2: Chemical
ChemComp-C21 / THIOPHENE-2-CARBOXYLIC ACID


Mass: 128.149 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4O2S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 % PEG 3350, 0.1 M Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.72→39.58 Å / Num. obs: 99134 / % possible obs: 97.57 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.079 / Net I/σ(I): 21.84
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.97 / Rsym value: 0.417 / % possible all: 80

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Processing

Software
NameVersionClassification
HKL-2000data collection
MolRepmodel building
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MolRepphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V7B

2v7b


Resolution: 1.72→39.58 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.364 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19366 5270 5 %RANDOM
Rwork0.15654 ---
obs0.1584 99134 97.57 %-
all-541417 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.72→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7880 0 74 572 8526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0198236
X-RAY DIFFRACTIONr_bond_other_d0.0010.027744
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.97511228
X-RAY DIFFRACTIONr_angle_other_deg1.01317796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2551049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61822.959338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7711557
X-RAY DIFFRACTIONr_chiral_restr0.1830.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021887
X-RAY DIFFRACTIONr_mcbond_it2.1672.3874178
X-RAY DIFFRACTIONr_mcbond_other2.1662.3874177
X-RAY DIFFRACTIONr_mcangle_it2.9573.5675230
X-RAY DIFFRACTIONr_mcangle_other2.9573.5685231
X-RAY DIFFRACTIONr_scbond_it3.082.6744058
X-RAY DIFFRACTIONr_scbond_other3.0822.6754059
X-RAY DIFFRACTIONr_scangle_other4.4913.8955998
X-RAY DIFFRACTIONr_long_range_B_refined5.62719.9489379
X-RAY DIFFRACTIONr_long_range_B_other5.56419.7049173
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 315 -
Rwork0.26 5968 -
obs--80 %

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