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- PDB-8xsk: crystal structure of PPAT -

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Basic information

Entry
Database: PDB / ID: 8xsk
Titlecrystal structure of PPAT
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsYin, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: crystal structure of PPAT
Authors: Yin, H.S.
History
DepositionJan 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)35,3832
Polymers35,3832
Non-polymers00
Water1,20767
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)106,1496
Polymers106,1496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13590 Å2
ΔGint-143 kcal/mol
Surface area37640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.736, 78.736, 147.166
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 17691.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: coaD, kdtB, HP_1475 / Production host: Escherichia coli (E. coli)
References: UniProt: O26010, pantetheine-phosphate adenylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: sodium choloride, sodium acetate, Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Jan 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 24687 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.75 / Net I/σ(I): 36.9
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 2504 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OTW

3otw


Resolution: 1.98→27.02 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.896 / SU B: 3.583 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23082 1226 5.3 %RANDOM
Rwork0.17943 ---
obs0.18206 21969 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.295 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.27 Å2
Refinement stepCycle: 1 / Resolution: 1.98→27.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 67 2551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132536
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172428
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.6293422
X-RAY DIFFRACTIONr_angle_other_deg1.3961.575642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55222.931116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.7915466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4971510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5782.471254
X-RAY DIFFRACTIONr_mcbond_other2.5782.4681253
X-RAY DIFFRACTIONr_mcangle_it3.9213.6871564
X-RAY DIFFRACTIONr_mcangle_other3.923.6891565
X-RAY DIFFRACTIONr_scbond_it3.2512.8671282
X-RAY DIFFRACTIONr_scbond_other3.252.8691283
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9454.1361859
X-RAY DIFFRACTIONr_long_range_B_refined8.60347.27710381
X-RAY DIFFRACTIONr_long_range_B_other8.60447.27310366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.026 Å
RfactorNum. reflection% reflection
Rfree0.327 64 -
Rwork0.197 1213 -
obs--71.62 %

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