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- PDB-3nbk: Phosphopantetheine Adenylyltransferase from Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 3nbk
TitlePhosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis in complex with 4'-phosphopantetheine
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / PPAT / PhP / pantetheine / tuberculosis / phosphopantetheine adenylyltransferase
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / protein hexamerization / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsWubben, T.J. / Mesecar, A.D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Kinetic, thermodynamic, and structural insight into the mechanism of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis.
Authors: Wubben, T.J. / Mesecar, A.D.
History
DepositionJun 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_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_asym_id / _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_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_label_seq_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: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,87510
Polymers77,3244
Non-polymers1,5516
Water13,962775
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,31315
Polymers115,9876
Non-polymers2,3269
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area18010 Å2
ΔGint-174 kcal/mol
Surface area37690 Å2
MethodPISA
2
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
hetero molecules

C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
hetero molecules

C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,31315
Polymers115,9876
Non-polymers2,3269
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area20300 Å2
ΔGint-186 kcal/mol
Surface area37870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.627, 114.627, 135.206
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
Phosphopantetheine adenylyltransferase / Pantetheine-phosphate adenylyltransferase / PPAT / Dephospho-CoA pyrophosphorylase


Mass: 19331.111 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: coaD, kdtB, MT3043, MTCY349.22, Rv2965c, u0002e / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A530, UniProt: P9WPA5*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M Hepes pH 7 and 2.5 v/v % isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2009
RadiationMonochromator: double-crystal Si (111) sagittal focusing, vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→135.21 Å / Num. all: 141372 / Num. obs: 141259 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 32.9
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 3.4 / Num. unique all: 7008 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TFU

1tfu


Resolution: 1.58→135.21 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.081 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19906 7082 5 %RANDOM
Rwork0.18328 ---
obs0.18408 134177 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.58→135.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4903 0 90 775 5768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225009
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9816773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8785622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8223.241216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32315814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2561542
X-RAY DIFFRACTIONr_chiral_restr0.0830.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213734
X-RAY DIFFRACTIONr_mcbond_it0.7141.53121
X-RAY DIFFRACTIONr_mcangle_it1.3525038
X-RAY DIFFRACTIONr_scbond_it2.02731888
X-RAY DIFFRACTIONr_scangle_it3.4084.51735
LS refinement shellResolution: 1.577→1.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 516 -
Rwork0.256 9843 -
obs--99.95 %

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