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- PDB-1h1t: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Coenzyme A... -

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Basic information

Entry
Database: PDB / ID: 1h1t
TitlePHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Coenzyme A FROM ESCHERICHIA COLI
ComponentsPHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / COENZYME A BIOSYNTHESIS / 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
COENZYME A / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsIzard, T.
CitationJournal: J.Bacteriol. / Year: 2003
Title: A Novel Adenylate Binding Site Confers Phosphopantetheine Adenylyltransferase Interactions with Coenzyme A
Authors: Izard, T.
History
DepositionJul 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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)37,2298
Polymers35,7192
Non-polymers1,5106
Water5,152286
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)111,68824
Polymers107,1586
Non-polymers4,53018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPQS
Unit cell
Length a, b, c (Å)135.426, 135.426, 135.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 17859.625 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREVERSIBLY TRANSFERS AN ADENYLYL GROUP FROM ATP TO 4'- PHOSPHOPANTETHEINE, PRODUCING PYROPHOSPHATE ...REVERSIBLY TRANSFERS AN ADENYLYL GROUP FROM ATP TO 4'- PHOSPHOPANTETHEINE, PRODUCING PYROPHOSPHATE AND DEPHOSPHO-COA.

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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: 0.6 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion / Details: Izard, T., (1999) EMBO J., 18, 2021.
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: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 8, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→20 Å / Num. obs: 35949 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 12.351 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 17.8
Reflection shellResolution: 1.82→1.82 Å / Rmerge(I) obs: 0.495 / % possible all: 77.8
Reflection
*PLUS
Highest resolution: 1.78 Å / Num. obs: 39181 / % possible obs: 99 % / Num. measured all: 815367 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 1.84 Å / % possible obs: 90.7 % / Rmerge(I) obs: 0.257

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 1B6T

1b6t


Resolution: 1.78→21.97 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1960 5 %RANDOM
Rwork0.218 ---
obs0.218 39134 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0571 Å2 / ksol: 0.378372 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.78→21.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 90 286 2857
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.61.5
X-RAY DIFFRACTIONc_mcangle_it1.072
X-RAY DIFFRACTIONc_scbond_it0.82
X-RAY DIFFRACTIONc_scangle_it1.252.5
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 343 5.3 %
Rwork0.302 5860 -
obs--90.7 %
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
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
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_deg0.84
LS refinement shell
*PLUS
Rfactor Rfree: 0.302 / Rfactor Rwork: 0.323

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