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- PDB-3rhs: Phosphopantetheine adenylyltransferase from Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 3rhs
TitlePhosphopantetheine adenylyltransferase from Mycobacterium tuberculosis complexed with CoA
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / coa
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
COENZYME A / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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
Authors: Timofeev, V.I. / Smirnova, E.A. / Chupova, L.A. / Esipov, R.S. / Kuranova, I.P.
History
DepositionApr 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9272
Polymers17,1601
Non-polymers7681
Water1,13563
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)107,56412
Polymers102,9586
Non-polymers4,6056
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation16_454y-2/3,x+2/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area19360 Å2
ΔGint-127 kcal/mol
Surface area37690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.886, 98.886, 114.869
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-211-

HOH

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Components

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


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 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A530, UniProt: P9WPA5*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAUTHORS STATE THAT LIGAND-FERMENT INTERACTION BETWEEN THE STARTING COMPOUND COENZYME A (LIGAND CODE ...AUTHORS STATE THAT LIGAND-FERMENT INTERACTION BETWEEN THE STARTING COMPOUND COENZYME A (LIGAND CODE COA) AND PROTEIN ENVIRONMENT (FERMENT INTERACTION) CAUSED GEOMETRIC CHANGES IN THE LIGAND STRUCTURE AND THE FINAL PRODUCT IA8 WAS OBSERVED IN THE CRYSTAL STRUCTURE

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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: 3.15 Å3/Da / Density % sol: 60.94 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8
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: 1.5→40 Å / Num. obs: 34704 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.048

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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 / Resolution: 1.59→9.7 Å / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 1374 5 %
Rwork0.2098 --
obs0.212 26812 92.21 %
all-26812 -
Refinement stepCycle: LAST / Resolution: 1.59→9.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 48 63 1312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041305
X-RAY DIFFRACTIONf_angle_d0.9241783
X-RAY DIFFRACTIONf_dihedral_angle_d18.413513
X-RAY DIFFRACTIONf_chiral_restr0.061204
X-RAY DIFFRACTIONf_plane_restr0.019229

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