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- PDB-4u89: 4'-phosphopantetheinyl transferase PptT from Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 4u89
Title4'-phosphopantetheinyl transferase PptT from Mycobacterium tuberculosis
ComponentsPhosphopantetheinyl transferase PptT
KeywordsTRANSFERASE
Function / homology
Function and homology information


siderophore metabolic process / enterobactin synthetase complex / holo-[acyl-carrier-protein] synthase / enterobactin biosynthetic process / siderophore biosynthetic process / holo-[acyl-carrier-protein] synthase activity / magnesium ion binding / plasma membrane
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 / IMIDAZOLE / PHOSPHATE ION / 4'-phosphopantetheinyl transferase PptT
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsFaille, A. / Mourey, L. / Pedelacq, J.D.
CitationJournal: to be published
Title: X-ray structure of the 4'-phosphopantetheinyl transferase PptT from Mycobacterium tuberculosis
Authors: Faille, A. / Gavalda, S. / Rottier, K. / Mourey, L. / Pedelacq, J.D.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,15016
Polymers27,7721
Non-polymers1,37915
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-94 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.808, 121.263, 48.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphopantetheinyl transferase PptT / Phosphopantetheinyl transferase PptT (CoA:APO-[ACP]pantetheinephosphotransferase) (CoA:APO-[acyl- ...Phosphopantetheinyl transferase PptT (CoA:APO-[ACP]pantetheinephosphotransferase) (CoA:APO-[acyl-carrier protein]pantetheinephosphotransferase)


Mass: 27771.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: pptT, Rv2794c, P425_02911, RVBD_2794c / Plasmid: pTet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O33336

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Non-polymers , 6 types, 286 molecules

#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


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


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.67 Å3/Da / Density % sol: 53.9 % / Description: platelets
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 22% PEG 1000, 0.2 M LiSO4, 0.1 M phosphate-citrate pH 4.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.98011
SYNCHROTRONESRF ID2922.0664
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 9, 2012
DECTRIS PILATUS 6M2PIXEL
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.980111
22.06641
ReflectionNumber: 685637 / Rmerge(I) obs: 0.097 / Χ2: 0.88 / D res high: 2 Å / Num. obs: 32126 / % possible obs: 82.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
8.9530.31643910.052
6.338.9579910.055
5.176.33102210.06
4.475.17123310.055
44.47136110.057
3.654153910.062
3.383.65167110.068
3.163.38179310.076
2.983.16187110.09
2.832.98202310.102
2.72.83206310.121
2.582.7218510.148
2.482.58227310.182
2.392.48232910.221
2.312.39230710.287
2.242.31235410.424
2.172.24200110.796
2.112.17140812.13
2.052.111023134.312
22.054321
ReflectionResolution: 1.4→30.316 Å / Num. obs: 58569 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.98 % / Biso Wilson estimate: 21.864 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.074 / Χ2: 1.011 / Net I/σ(I): 15.12 / Num. measured all: 408859
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.4-1.480.8660.5142.7348946940192610.5798.5
1.48-1.590.9630.3175.1762331880988090.341100
1.59-1.710.9830.2038.0460662824382420.218100
1.71-1.880.9930.13112.0356252760276010.141100
1.88-2.10.9960.08718.3150511689268900.093100
2.1-2.420.9970.06924.2345263610861060.074100
2.42-2.960.9970.05929.3838765519851970.063100
2.96-4.180.9980.05135.0529631410041000.055100
4.18-30.3160.9960.04936.616498237123630.05399.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
REFMAC5.6.0117refinement
XSCALEdata scaling
SHELXDphasing
XSCALEdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.4→30.32 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1611 / WRfactor Rwork: 0.1364 / FOM work R set: 0.9134 / SU B: 1.538 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0485 / SU Rfree: 0.0469 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1663 2964 5.1 %RANDOM
Rwork0.1384 55599 --
obs0.1398 58563 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.09 Å2 / Biso mean: 20.226 Å2 / Biso min: 8.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.4→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 82 271 2066
Biso mean--27.74 36.93 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021959
X-RAY DIFFRACTIONr_angle_refined_deg2.4152.0152706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3622.05573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05215304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4131518
X-RAY DIFFRACTIONr_chiral_restr0.1580.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0221485
X-RAY DIFFRACTIONr_rigid_bond_restr8.27331958
X-RAY DIFFRACTIONr_sphericity_free38.913586
X-RAY DIFFRACTIONr_sphericity_bonded17.02152092
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 214 -
Rwork0.339 3730 -
all-3944 -
obs--96.6 %

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