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- PDB-4qjl: Crystal structure of M. ulcerans phosphopantetheinyl transferase MuPPT -

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Basic information

Entry
Database: PDB / ID: 4qjl
TitleCrystal structure of M. ulcerans phosphopantetheinyl transferase MuPPT
ComponentsPhosphopantetheinyl transferase, PptII
KeywordsTRANSFERASE / Phosphopantetheinyl Transferase / CoA Binding
Function / homology
Function and homology information


enterobactin synthetase complex / enterobactin biosynthetic process / holo-[acyl-carrier-protein] synthase activity / magnesium ion binding
Similarity search - Function
Enterobactin synthetase-like, component D / 4'-phosphopantetheinyl transferase, N-terminal domain / 4'-phosphopantetheinyl transferase N-terminal domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily
Similarity search - Domain/homology
COENZYME A / Phosphopantetheinyl transferase, PptII
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNoel, J.P. / Burkart, M.D. / Vickery, C.R.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structure, biochemistry, and inhibition of essential 4'-phosphopantetheinyl transferases from two species of mycobacteria.
Authors: Vickery, C.R. / Kosa, N.M. / Casavant, E.P. / Duan, S. / Noel, J.P. / Burkart, M.D.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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.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

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Assembly

Deposited unit
A: Phosphopantetheinyl transferase, PptII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5303
Polymers25,7381
Non-polymers7922
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.020, 59.750, 74.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphopantetheinyl transferase, PptII


Mass: 25738.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: MUL_2141, MuPPT, pptII, YP_906028 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 DE3
References: UniProt: A0PQD8, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2 M lithium chloride, 32% (w/v) PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 30279 / Num. obs: 25868 / % possible obs: 85.5 % / Biso Wilson estimate: 14.8 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
5.22-407.20.06920.31074199.7
3.69-5.227.30.08920.518151100
3.01-3.697.30.1216.623231100
2.61-3.017.70.17112.426971100
2.33-2.617.70.2749.530511100
2.13-2.336.10.3227.433431100
1.97-2.135.50.38963377193.5
1.84-1.9730.195.12560166.9
1.74-1.8430.2753.52749167.1
1.65-1.742.70.3882.32879166.7

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
BOSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→37.24 Å / SU ML: 0.18 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 1285 4.98 %random
Rwork0.1599 ---
obs0.1623 25814 85.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.46 Å2 / Biso mean: 21.0909 Å2 / Biso min: 5.35 Å2
Refinement stepCycle: LAST / Resolution: 1.65→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 49 229 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0311863
X-RAY DIFFRACTIONf_angle_d1.4452557
X-RAY DIFFRACTIONf_chiral_restr0.051287
X-RAY DIFFRACTIONf_plane_restr0.007325
X-RAY DIFFRACTIONf_dihedral_angle_d15.655683
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.71610.28241060.24932082218866
1.7161-1.79420.23481140.20722065217966
1.7942-1.88880.24141080.18222108221666
1.8888-2.00710.20131060.17352144225068
2.0071-2.16210.2471670.178231593326100
2.1621-2.37960.23781750.17131713346100
2.3796-2.72380.19831670.161932033370100
2.7238-3.43140.21591650.149232303395100
3.4314-37.24950.17171770.135533673544100

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