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

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Basic information

Entry
Database: PDB / ID: 3rba
TitlePhosphopantetheine adenylyltransferase from Mycobacterium tuberculosis complexed with DPCoA
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / dpcoa
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
DEPHOSPHO 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 Tuberculosis in the Apo Form and in Complexes with Coenzyme A and Dephosphocoenzyme A
Authors: Timofeev, V.I. / Smirnova, E.A. / Chupova, L.A. / Esipov, R.S. / Kuranova, I.P.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8472
Polymers17,1601
Non-polymers6881
Water1,15364
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)107,08412
Polymers102,9586
Non-polymers4,1256
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area22000 Å2
ΔGint-174 kcal/mol
Surface area34690 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5426
Polymers51,4793
Non-polymers2,0633
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7280 Å2
ΔGint-65 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.224, 99.224, 115.852
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-179-

HOH

21A-193-

HOH

31A-207-

HOH

41A-219-

HOH

51A-220-

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 / 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: Chemical ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H35N7O13P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growDetails: counter diffusion

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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 315 / Detector: CCD / Date: Nov 10, 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. all: 35955 / Num. obs: 35955 / % possible obs: 98.8 % / Rmerge(I) obs: 0.049

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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 code 1TFU

1tfu


Resolution: 1.59→11.406 Å / σ(F): 3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 1413 5.02 %RANDOM
Rwork0.1566 ---
obs0.1592 28160 95.31 %-
all-28160 --
Refinement stepCycle: LAST / Resolution: 1.59→11.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 44 64 1309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.004

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