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- PDB-1qjc: Phosphopantetheine Adenylyltransferase from Escherichia coli in c... -

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Basic information

Entry
Database: PDB / ID: 1qjc
TitlePhosphopantetheine Adenylyltransferase from Escherichia coli in complex with 4'-phosphopantetheine
ComponentsPHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
KeywordsCOENZYME A BIOSYNTHESIS / TRANSFERASE / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein 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
4'-PHOSPHOPANTETHEINE / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsIzard, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The Crystal Structures of Phosphopantetheine Adenylyltransferase with Bound Substrates Reveal the Enzyme'S Catalytic Mechanism
Authors: Izard, T.
History
DepositionJun 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 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
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2968
Polymers35,4572
Non-polymers8396
Water4,990277
1
A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules

A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules

A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,88724
Polymers106,3716
Non-polymers2,51618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18260 Å2
ΔGint-142.8 kcal/mol
Surface area42370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)135.331, 135.331, 135.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.066398, 0.128795, -0.989446), (0.084424, -0.987353, -0.134188), (-0.994215, -0.092443, 0.054685)
Vector: 63.9004, 67.7114, 67.0611)
DetailsBIOLOGICAL_UNIT: HOMOHEXAMER

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Components

#1: Protein PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE / PPAT / PANTETHEINE-PHOSPHATE ADENYLYLTRANSFERASE / DEPHOSPHO-COA PYROPHOSPHORYLASE


Mass: 17728.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli)
References: UniProt: P23875, UniProt: P0A6I6*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: REVERSIBLY TRANSFERS AN ADENYLYL GROUP FROM ATP TO 4'- PHOSPHOPANTETHEINE, YIELDING ...FUNCTION: REVERSIBLY TRANSFERS AN ADENYLYL GROUP FROM ATP TO 4'- PHOSPHOPANTETHEINE, YIELDING DEPHOSPHO-COA (DPCOA) AND PYROPHOSPHATE. CATALYTIC ACTIVITY: ATP + PANTETHEINE 4'-PHOSPHATE = DIPHOSPHATE + DEPHOSPHO-COA. PATHWAY: COENZYME A (COA) BIOSYNTHESIS; FOURTH STEP. SUBUNIT: HOMOHEXAMER. SUBCELLULAR LOCATION: CYTOPLASMIC. SIMILARITY: BELONGS TO THE COAD FAMILY.

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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: 2.88 Å3/Da / Density % sol: 57 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorDetector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 33838 / % possible obs: 86.3 % / Observed criterion σ(I): 1 / Redundancy: 20.02 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 44.2
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.409 / % possible all: 51.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B6T

1b6t


Resolution: 1.63→67.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3212744.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2569 5.1 %RANDOM
Rwork0.216 ---
obs0.216 50637 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.226 Å2 / ksol: 0.363602 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.63→67.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 47 277 2796
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it1.392
X-RAY DIFFRACTIONc_scangle_it2.12.5
LS refinement shellResolution: 1.63→1.73 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 420 5.4 %
Rwork0.301 7387 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER-TOPOLOGY
X-RAY DIFFRACTION3PNS.PARPNS.TOP

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