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- PDB-1gn8: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Mn2+ATP FR... -

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Basic information

Entry
Database: PDB / ID: 1gn8
TitlePHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Mn2+ATP FROM ESCHERICHIA COLI
ComponentsPHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / COENZYME A BIOSYNTHESIS / NUCLEOTIDYLTRANSFERASE
Function / homologyPhosphopantetheine adenylyltransferase / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold / Cytidylyltransferase-like / pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein binding / cytoplasm ...Phosphopantetheine adenylyltransferase / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold / Cytidylyltransferase-like / pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein binding / cytoplasm / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Function and homology information
Specimen sourceESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.83 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2001 / Release: Jan 17, 2002
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 17, 2002Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jun 28, 2017Structure modelData collectiondiffrn_source_diffrn_source.type

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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)37,1329
Polyers35,7192
Non-polymers1,4127
Water4,450247
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)111,39527
Polyers107,1586
Non-polymers4,23721
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)135.060, 135.060, 135.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI 2 3

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Components

#1: Protein/peptide PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE


Mass: 17859.625 Da / Num. of mol.: 2 / 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.: 3 / Formula: SO4 / Sulfate
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Formula: Mn / Manganese
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Formula: H2O / Water

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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 / Density percent sol: 60 %
Crystal growpH: 5 / Details: pH 5.00
Crystal
*PLUS
Density percent sol: 57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Izard, T., (1999) Acta Crystallog., D55, 1226. / pH: 8
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
110 mMHEPESdroppH8.
20.5 mMdithiothreitoldrop
318 mg/mlproteindrop
41.1 Mammonium sulfatereservoir
50.2 MreservoirNaCl
6100 mMsodium acetatereservoirpH5.

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Jul 21, 2000
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 21.4 Å2 / D resolution high: 1.82 Å / D resolution low: 2 Å / Number obs: 35949 / Observed criterion sigma I: 1 / Rmerge I obs: 0.163 / NetI over sigmaI: 17.8 / Redundancy: 12.351 % / Percent possible obs: 97.1
Reflection shellRmerge I obs: 0.495 / Highest resolution: 1.82 Å / Lowest resolution: 1.82 Å / Percent possible all: 77.8
Reflection
*PLUS
Number measured all: 444009 / Percent possible obs: 96.9 / Rmerge I obs: 0.107
Reflection shell
*PLUS
Percent possible obs: 77.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 1B6T
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL
Displacement parametersB iso mean: 26.6 Å2 / Aniso B11: 0 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0 Å2
Least-squares processR factor R free: 0.245 / R factor R free error: 0.005 / R factor R work: 0.229 / R factor obs: 0.229 / Highest resolution: 1.83 Å / Lowest resolution: 21.91 Å / Number reflection R free: 1774 / Number reflection obs: 35800 / Percent reflection R free: 5 / Percent reflection obs: 99
Refine analyzeLuzzati coordinate error free: 0.28 Å / Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.28 Å / Luzzati sigma a obs: 0.3 Å
Refine hist #LASTHighest resolution: 1.83 Å / Lowest resolution: 21.91 Å
Number of atoms included #LASTProtein: 2506 / Nucleic acid: 0 / Ligand: 79 / Solvent: 247 / Total: 2832
Refine LS restraints
Refine IDTypeDev ideal
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_deg1.20
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.40
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS shellHighest resolution: 1.83 Å / R factor R free: 0.319 / R factor R free error: 0.019 / R factor R work: 0.338 / Lowest resolution: 1.94 Å / Number reflection R free: 282 / Number reflection R work: 5625 / Total number of bins used: 6 / Percent reflection R free: 5.3 / Percent reflection obs: 98.7
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER-TOPOLOGY
X-RAY DIFFRACTION3DPC.PARDPC.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Displacement parameters
*PLUS
B iso mean: 24.6 Å2
Least-squares process
*PLUS
Number reflection obs: 35859
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.40
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
Refine LS shell
*PLUS
R factor obs: 0.338

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