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- PDB-5t81: Rhombohedral crystal form of the EpoB NRPS cyclization-docking bi... -

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Basic information

Entry
Database: PDB / ID: 5t81
TitleRhombohedral crystal form of the EpoB NRPS cyclization-docking bidomain from Sorangium cellulosum
ComponentsEpoB
KeywordsBIOSYNTHETIC PROTEIN / epothilone / NRPS / thiazoline / cyclization
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / oxidoreductase activity / cytoplasm
Similarity search - Function
TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Nitroreductase / Nitroreductase family / Nitroreductase-like / Condensation domain / Condensation domain / Amino acid adenylation domain / Chloramphenicol acetyltransferase-like domain superfamily ...TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Nitroreductase / Nitroreductase family / Nitroreductase-like / Condensation domain / Condensation domain / Amino acid adenylation domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.604 Å
AuthorsDowling, D.P. / Kung, Y. / Croft, A.K. / Taghizadeh, K. / Kelly, W.L. / Walsh, C.T. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural elements of an NRPS cyclization domain and its intermodule docking domain.
Authors: Dowling, D.P. / Kung, Y. / Croft, A.K. / Taghizadeh, K. / Kelly, W.L. / Walsh, C.T. / Drennan, C.L.
History
DepositionSep 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EpoB
B: EpoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6213
Polymers123,5282
Non-polymers921
Water2,936163
1
A: EpoB


Theoretical massNumber of molelcules
Total (without water)61,7641
Polymers61,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EpoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8562
Polymers61,7641
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.836, 159.836, 318.679
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein EpoB


Mass: 61764.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Gene: epoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KIZ9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNcoI restriction site was used for the original cloning into pET30a, introducing an Ala ...NcoI restriction site was used for the original cloning into pET30a, introducing an Ala substitution for Thr at position two

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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: 3.41 Å3/Da / Density % sol: 63.88 % / Description: Rhombohedral crystals formed after 4 weeks.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: reservoir of 56% tacsimate (pH 7.0; Hampton Research, Aliso Viejo, CA) and 1% PEG 1,500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 47986 / % possible obs: 99.7 % / Redundancy: 3 % / Rsym value: 0.062 / Net I/σ(I): 40.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
SOLVEphasing
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2.604→43.732 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 2403 5.01 %5%
Rwork0.1893 ---
obs0.1911 47967 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.98 Å2 / Biso mean: 53.3089 Å2 / Biso min: 29.9 Å2
Refinement stepCycle: final / Resolution: 2.604→43.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8067 0 6 163 8236
Biso mean--50 45.17 -
Num. residues----1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058325
X-RAY DIFFRACTIONf_angle_d0.74911332
X-RAY DIFFRACTIONf_chiral_restr0.0321283
X-RAY DIFFRACTIONf_plane_restr0.0041478
X-RAY DIFFRACTIONf_dihedral_angle_d12.9483190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.604-2.65710.32981490.28992556270596
2.6571-2.71490.3431290.270326672796100
2.7149-2.77810.30021290.264526262755100
2.7781-2.84750.32991330.265426642797100
2.8475-2.92450.31111320.256926892821100
2.9245-3.01050.29661280.254726752803100
3.0105-3.10770.28011390.245626522791100
3.1077-3.21870.26861490.246426652814100
3.2187-3.34750.3061360.239326782814100
3.3475-3.49980.27761490.221126782827100
3.4998-3.68430.23271480.207426612809100
3.6843-3.9150.21391590.182726902849100
3.915-4.2170.22431660.168426472813100
4.217-4.6410.17481450.147127102855100
4.641-5.31150.17641310.141127332864100
5.3115-6.68810.18061370.17227442881100
6.6881-43.73810.16471440.13572829297399

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