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- PDB-1b6t: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH 3'-DEPHOSP... -

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Basic information

Entry
Database: PDB / ID: 1b6t
TitlePHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH 3'-DEPHOSPHO-COA FROM ESCHERICHIA COLI
ComponentsPROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
KeywordsTRANSFERASE / COENZYME A BIOSYNTHESIS
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
DEPHOSPHO COENZYME A / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsIzard, T.
CitationJournal: EMBO J. / Year: 1999
Title: The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity.
Authors: Izard, T. / Geerlof, A.
History
DepositionJan 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
B: PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6956
Polymers35,7192
Non-polymers9764
Water5,801322
1
A: PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
B: PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
hetero molecules

A: PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
B: PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
hetero molecules

A: PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
B: PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,08518
Polymers107,1586
Non-polymers2,92712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)135.500, 135.500, 135.500
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)

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Components

#1: Protein PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE) / E.C.2.7.7.3 TRANSFERASE / PPAT / KDTB


Mass: 17859.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0A6I6, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COD / DEPHOSPHO COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.88 Å3/Da / Density % sol: 0.57 %
Crystal growpH: 5 / Details: pH 5.
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
210 mMHEPES1drop
30.5 mMdithiothreitol1drop
41.1 Mammonium sulfate1reservoir
50.2 M1reservoirNaCl
6100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.978418,0.978668 ,0.95
DetectorType: BRANDEIS / Detector: CCD / Date: Jul 15, 1998 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9784181
20.9786681
30.951
ReflectionResolution: 1.8→20 Å / Num. obs: 48585 / % possible obs: 0.994 % / Observed criterion σ(I): 1 / Redundancy: 14 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 21.7
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.239 / % possible all: 0.958
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 36339 / % possible obs: 94.7 % / Redundancy: 15.1 % / Num. measured all: 547185
Reflection shell
*PLUS
% possible obs: 95.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→23.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3664358.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1892 5 %RANDOM
Rwork0.205 ---
obs0.222 37468 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.3718 Å2 / ksol: 0.406625 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 59 322 2853
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 294 5.3 %
Rwork0.275 5236 -
obs--86.9 %
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 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.275

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