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- PDB-2cb9: Crystal structure of the thioesterase domain of the fengycin bios... -

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Basic information

Entry
Database: PDB / ID: 2cb9
TitleCrystal structure of the thioesterase domain of the fengycin biosynthesis cluster
ComponentsFENGYCIN SYNTHETASE
KeywordsHYDROLASE / THIOESTERASE / NON-RIBOSOMAL PEPTIDE SYNTHESIS / ALPHA/BETA-HYDROLASES / CATALYTIC TRIADE
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
cAMP-dependent Protein Kinase, Chain A - #10 / cAMP-dependent Protein Kinase, Chain A / AMP-binding / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain ...cAMP-dependent Protein Kinase, Chain A - #10 / cAMP-dependent Protein Kinase, Chain A / AMP-binding / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Helix non-globular / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Special / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Fengycin synthetase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSamel, S. / Marahiel, M.A. / Essen, L.-O.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Thioesterase Domain of the Fengycin Biosynthesis Cluster: A Structural Base for the Macrocyclization of a Non-Ribosomal Lipopeptide
Authors: Samel, S. / Wagner, B. / Marahiel, M.A. / Essen, L.-O.
History
DepositionJan 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FENGYCIN SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5832
Polymers27,5231
Non-polymers601
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.354, 72.354, 96.333
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein FENGYCIN SYNTHETASE


Mass: 27522.734 Da / Num. of mol.: 1 / Fragment: THIOESTERASE DOMAIN RESIDUES 1043-1274
Source method: isolated from a genetically manipulated source
Details: RECOMBINANT FRAGMENT OF THE NRPS SYNTHETASE FENB (Q1043-H1274)
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: F29-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4 / References: UniProt: Q45563
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.6
Details: 0.2 M NH4 ACETATE; 0.1 M NA CITRATE (PH 5.6); 22.5 % PEG 8000, 10 MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2003 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→24 Å / Num. obs: 26374 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JMK

1jmk


Resolution: 1.8→24.35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.862 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES T123-S129 WERE DISORDERED AND OMITTED FROM THE STRUCTURAL MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1337 5.1 %RANDOM
Rwork0.15 ---
obs0.152 24923 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 4 353 2032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211711
X-RAY DIFFRACTIONr_bond_other_d0.0020.021506
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9422307
X-RAY DIFFRACTIONr_angle_other_deg0.83933520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021932
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02339
X-RAY DIFFRACTIONr_nbd_refined0.2420.2379
X-RAY DIFFRACTIONr_nbd_other0.2490.21802
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.2987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1311.51048
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08921667
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.153663
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1974.5640
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 81
Rwork0.26 1682

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