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- PDB-3flb: RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic ... -

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Basic information

Entry
Database: PDB / ID: 3flb
TitleRifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 2
ComponentsRifR
KeywordsHYDROLASE / alpha-beta hydrolase thioesterase
Function / homology
Function and homology information


lipid biosynthetic process / hydrolase activity
Similarity search - Function
Thioesterase type II, NRPS/PKS/S-FAS / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAmycolatopsis mediterranei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSmith, J.L. / Akey, D.L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and Functional Analysis of RifR, the Type II Thioesterase from the Rifamycin Biosynthetic Pathway.
Authors: Claxton, H.B. / Akey, D.L. / Silver, M.K. / Admiraal, S.J. / Smith, J.L.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RifR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4923
Polymers29,2621
Non-polymers2302
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.938, 62.497, 82.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RifR


Mass: 29262.340 Da / Num. of mol.: 1 / Mutation: S94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei (bacteria) / Gene: rifR / Plasmid: pET21,pMS25 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q7BUF9, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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 % sol: 28.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES pH 7.0, 12% PEG 8000, 50 mM CaCl2, 2 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 10, 2008 / Details: APS Beamline 23-ID-D
RadiationMonochromator: APS Beamline 23-ID-D / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 19447 / Num. obs: 18683 / % possible obs: 96.1 % / Redundancy: 2.9 % / Rsym value: 0.069 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.376 / % possible all: 88.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.68 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 957 5.1 %RANDOM
Rwork0.1859 ---
obs0.18862 17702 96.43 %-
all-19447 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---1.41 Å20 Å2
3---1.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 14 167 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9842708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9395253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.50221.20991
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5515303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5891527
X-RAY DIFFRACTIONr_chiral_restr0.0780.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021571
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21026
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21347
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.35851277
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.41382012
X-RAY DIFFRACTIONr_scbond_it2.1775776
X-RAY DIFFRACTIONr_scangle_it2.8085696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 63 -
Rwork0.249 1179 -
obs--89.29 %

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