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- PDB-4mrt: Structure of the Phosphopantetheine Transferase Sfp in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 4mrt
TitleStructure of the Phosphopantetheine Transferase Sfp in Complex with Coenzyme A and a Peptidyl Carrier Protein
Components
  • 4'-phosphopantetheinyl transferase sfp
  • Tyrocidine synthase 3
KeywordsTRANSPORT PROTEIN/TRANSFERASE / PCP: Aminoacyl/peptidyl carrier / Sfp: Phosphopantetheine transferase / Sfp: Coenzyme A binding / TRANSPORT PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


positive regulation of single-species biofilm formation / holo-[acyl-carrier-protein] synthase / amide biosynthetic process / lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / secondary metabolite biosynthetic process / organonitrogen compound biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / ligase activity ...positive regulation of single-species biofilm formation / holo-[acyl-carrier-protein] synthase / amide biosynthetic process / lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / secondary metabolite biosynthetic process / organonitrogen compound biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
4'-phosphopantetheinyl transferase domain / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / ACP-like / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Ribosomal Protein L22; Chain A ...4'-phosphopantetheinyl transferase domain / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / ACP-like / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Ribosomal Protein L22; Chain A / Condensation domain / Condensation domain / Amino acid adenylation domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Tyrocidine synthase 3 / 4'-phosphopantetheinyl transferase Sfp
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
Bacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsTufar, P. / Rahighi, S. / Kraas, F.I. / Kirchner, D.K. / Loehr, F. / Henrich, E. / Koepke, J. / Dikic, I. / Guentert, P. / Marahiel, M.A. / Doetsch, V.
CitationJournal: Chem.Biol. / Year: 2014
Title: Crystal Structure of a PCP/Sfp Complex Reveals the Structural Basis for Carrier Protein Posttranslational Modification.
Authors: Tufar, P. / Rahighi, S. / Kraas, F.I. / Kirchner, D.K. / Lohr, F. / Henrich, E. / Kopke, J. / Dikic, I. / Guntert, P. / Marahiel, M.A. / Dotsch, V.
History
DepositionSep 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
C: Tyrocidine synthase 3
A: 4'-phosphopantetheinyl transferase sfp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2237
Polymers37,2182
Non-polymers1,0045
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-51 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.660, 39.090, 53.310
Angle α, β, γ (deg.)90.000, 107.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules CA

#1: Protein Tyrocidine synthase 3 / Tyrocidine synthase III / ATP-dependent asparagine adenylase / AsnA / Asparagine activase / ATP- ...Tyrocidine synthase III / ATP-dependent asparagine adenylase / AsnA / Asparagine activase / ATP-dependent glutamine adenylase / GlnA / Glutamine activase / ATP-dependent tyrosine adenylase / TyrA / Tyrosine activase / ATP-dependent valine adenylase / ValA / Valine activase / ATP-dependent ornithine adenylase / OrnA / Ornithine activase / ATP-dependent leucine adenylase / LeuA / Leucine activase


Mass: 9972.424 Da / Num. of mol.: 1
Fragment: Peptidyl carrier protein domain(UNP Residues 3038-3113)
Mutation: S3075A
Source method: isolated from a genetically manipulated source
Details: Cytosol / Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Strain: ATCC 8185 / Gene: tycC / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4) / References: UniProt: O30409
#2: Protein 4'-phosphopantetheinyl transferase sfp / Surfactin synthase-activating enzyme


Mass: 27245.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cytosol
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU03570, lpa-8, sfp / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4)
References: UniProt: P39135, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups

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Non-polymers , 5 types, 177 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16 M magnesium acetate, 0.08 M sodium cacodylate, 16% (w/v) PEG 8000, 20% (v/v) glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2012
Details: The optical elements consist of a vertically collimating mirror (M1, focus at infinity), followed by a Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry, and a ...Details: The optical elements consist of a vertically collimating mirror (M1, focus at infinity), followed by a Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry, and a toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification).
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→37.91 Å / Num. all: 21610 / Num. obs: 21594 / % possible obs: 99.45 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Net I/σ(I): 6.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
go.comdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.91 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2531 / WRfactor Rwork: 0.2036 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8521 / SU B: 4.467 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1998 / SU Rfree: 0.1709 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1101 5.1 %RANDOM
Rwork0.1883 ---
obs0.1906 21592 99.19 %-
all-21610 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.62 Å2 / Biso mean: 29.0043 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å2-2.18 Å2
2--3.12 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 61 172 2662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192548
X-RAY DIFFRACTIONr_bond_other_d0.0010.022386
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9883452
X-RAY DIFFRACTIONr_angle_other_deg0.78635510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29423.761117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64915434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4891515
X-RAY DIFFRACTIONr_chiral_restr0.1780.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02581
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 77 -
Rwork0.241 1516 -
all-1593 -
obs--98.58 %

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