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- PDB-3rff: Phosphopantetheine adenylyltransferase from Mycobacterium Tubercu... -

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Basic information

Entry
Database: PDB / ID: 3rff
TitlePhosphopantetheine adenylyltransferase from Mycobacterium Tuberculosis (1.76 A resolution)
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsTimofeev, V.I. / Smirnova, E.A. / Chupova, L.A. / Esipov, R.S. / Kuranova, I.P.
CitationJournal: Crystallography Reports / Year: 2012
Title: Three-Dimensional Structure of Phosphopantetheine Adenylyltransferase from Mycobacterium Tuberculosis in the Apo Form and in Complexes with Coenzyme A and D
Authors: Timofeev, V.I. / Smirnova, E.A. / Chupova, L.A. / Esipov, R.S. / Kuranova, I.P.
History
DepositionApr 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
Water1,04558
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_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area13260 Å2
ΔGint-98 kcal/mol
Surface area37750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.678, 98.678, 113.855
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 17159.738 Da / Num. of mol.: 1 / Fragment: unp residues 1-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: coaD, kdtB, Rv2965c, MT3043, MTCY349.22, u0002e / 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.: 58 / 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: 3.11 Å3/Da / Density % sol: 60.43 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 28293 / Num. obs: 28293 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TFU

1tfu


Resolution: 1.76→7.995 Å / σ(F): 1.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1003 5.09 %random
Rwork0.1747 ---
obs0.1772 19710 93.54 %-
all-19710 --
Refinement stepCycle: LAST / Resolution: 1.76→7.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 0 58 1259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061230
X-RAY DIFFRACTIONf_angle_d0.8891669
X-RAY DIFFRACTIONf_dihedral_angle_d15.512449
X-RAY DIFFRACTIONf_chiral_restr0.058196
X-RAY DIFFRACTIONf_plane_restr0.004219

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