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- PDB-1tfu: phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1tfu
Titlephosphopantetheine adenylyltransferase from Mycobacterium tuberculosis
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / TRANSPORT PROTEIN / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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
Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMorris, V.K. / Izard, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Protein Sci. / Year: 2004
Title: Substrate-induced asymmetry and channel closure revealed by the apoenzyme structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase.
Authors: Morris, V.K. / Izard, T.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 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: Phosphopantetheine adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)17,1601
Polymers17,1601
Non-polymers00
Water2,378132
1
A: Phosphopantetheine adenylyltransferase
x 6


Theoretical massNumber of molelcules
Total (without water)102,9586
Polymers102,9586
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area13340 Å2
ΔGint-106 kcal/mol
Surface area38140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.623, 98.623, 114.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-158-

HOH

21A-172-

HOH

31A-174-

HOH

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Components

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


Mass: 17159.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: COAD, KDTB, RV2965C, MT3043, MTCY349.22, U0002E, MB2989C
Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A530, UniProt: P9WPA5*PLUS, pantetheine-phosphate adenylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.72 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.99→20 Å / Num. obs: 14805 / Redundancy: 28.2 % / Biso Wilson estimate: 18.6 Å2 / Net I/σ(I): 44.9

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→14.91 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3002981.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 749 5.1 %RANDOM
Rwork0.229 ---
all0.229 15554 --
obs0.229 14805 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.4071 Å2 / ksol: 0.355011 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0.75 Å20 Å2
2--0.08 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.99→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 0 132 1333
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.681.5
X-RAY DIFFRACTIONc_mcangle_it1.232
X-RAY DIFFRACTIONc_scbond_it0.852
X-RAY DIFFRACTIONc_scangle_it1.362.5
LS refinement shellResolution: 1.99→2.11 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 138 5.9 %
Rwork0.289 2204 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION4MPD.PAR
X-RAY DIFFRACTION5CAC.PAR

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