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- PDB-3uc5: Phosphopantetheine adenylyltransferase from Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 3uc5
TitlePhosphopantetheine adenylyltransferase from Mycobacterium tuberculosis complexed with ATP
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / PPAT / ATP-BINDING / COENZYME A BIOSYNTHESIS / NUCLEOTIDE-BINDING / NUCLEOTIDYLTRANSFERASE
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
ADENOSINE-5'-TRIPHOSPHATE / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTimofeev, V.I. / Smirnova, E.A. / Chupova, L.A. / Esipov, R.S. / Kuranova, I.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: X-ray study of the conformational changes in the molecule of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis during the catalyzed reaction.
Authors: Timofeev, V. / Smirnova, E. / Chupova, L. / Esipov, R. / Kuranova, I.
History
DepositionOct 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Sep 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

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6672
Polymers17,1601
Non-polymers5071
Water97354
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)106,00212
Polymers102,9586
Non-polymers3,0436
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
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area17910 Å2
ΔGint-113 kcal/mol
Surface area37550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.909, 99.909, 114.419
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-173-

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 / Plasmid: ER2566/pER-PPAT / Production host: Escherichia coli (E. coli)
References: UniProt: P0A530, UniProt: P9WPA5*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 61.59 %
Crystal growMethod: evaporation / Details: Counter diffusion, 12% MPD , EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 27524 / % possible obs: 93.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 68.312
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.509 / Rsym value: 0.441 / % possible all: 97.1

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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 3RFF

3rff


Resolution: 1.7→7.999 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1205 5.04 %random
Rwork0.1766 ---
obs0.179 23908 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 127.232 Å2 / ksol: 0.572 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3189 Å2-0 Å20 Å2
2---3.3189 Å2-0 Å2
3---4.4337 Å2
Refinement stepCycle: LAST / Resolution: 1.7→7.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 31 54 1286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061276
X-RAY DIFFRACTIONf_angle_d1.0921738
X-RAY DIFFRACTIONf_dihedral_angle_d17.246469
X-RAY DIFFRACTIONf_chiral_restr0.066201
X-RAY DIFFRACTIONf_plane_restr0.004223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.76740.2621140.19082495X-RAY DIFFRACTION98
1.7674-1.84690.23621200.17692455X-RAY DIFFRACTION98
1.8469-1.9430.23251330.15892503X-RAY DIFFRACTION99
1.943-2.06270.22361520.15992469X-RAY DIFFRACTION100
2.0627-2.21890.19361230.13872552X-RAY DIFFRACTION100
2.2189-2.43640.1831480.13852516X-RAY DIFFRACTION100
2.4364-2.7760.1981390.15922533X-RAY DIFFRACTION100
2.776-3.45010.1951340.15822560X-RAY DIFFRACTION100
3.4501-7.99920.23741420.19952620X-RAY DIFFRACTION100

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