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- PDB-8xrw: crystal structure of HpPPAT in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 8xrw
Titlecrystal structure of HpPPAT in complex with ATP
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / complex
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
ADENOSINE-5'-TRIPHOSPHATE / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 HpPPAT in complex with ATP
Authors: Yin, H.S.
History
DepositionJan 8, 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
I: Phosphopantetheine adenylyltransferase
J: Phosphopantetheine adenylyltransferase
L: Phosphopantetheine adenylyltransferase
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
G: Phosphopantetheine adenylyltransferase
H: Phosphopantetheine adenylyltransferase
K: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,82115
Polymers212,29912
Non-polymers1,5223
Water4,486249
1
I: Phosphopantetheine adenylyltransferase
J: Phosphopantetheine adenylyltransferase
L: Phosphopantetheine adenylyltransferase
G: Phosphopantetheine adenylyltransferase
H: Phosphopantetheine adenylyltransferase
K: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6719
Polymers106,1496
Non-polymers1,5223
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15910 Å2
ΔGint-128 kcal/mol
Surface area38130 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)106,1496
Polymers106,1496
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-133 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.150, 82.060, 105.512
Angle α, β, γ (deg.)88.02, 73.55, 87.14
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17691.580 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: ATP / 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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG1000, citrate phosphate, ATP, Li2SO4

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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 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→101.17 Å / Num. obs: 121952 / % possible obs: 97.8 % / Redundancy: 2 % / CC1/2: 0.925 / Net I/σ(I): 18.51
Reflection shellResolution: 2.12→2.2 Å / Num. unique obs: 121952 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OTW

3otw


Resolution: 2.2→101.17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.19 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24833 5330 5 %RANDOM
Rwork0.20316 ---
obs0.20533 102141 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.184 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.03 Å22.55 Å2
2--0.05 Å20.26 Å2
3---0.82 Å2
Refinement stepCycle: 1 / Resolution: 2.2→101.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14947 0 0 249 15196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01915265
X-RAY DIFFRACTIONr_bond_other_d0.0060.0214980
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.97220606
X-RAY DIFFRACTIONr_angle_other_deg0.905334546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53451862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13124.151636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.832152796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3431560
X-RAY DIFFRACTIONr_chiral_restr0.0970.22354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023416
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_it3.8563.997484
X-RAY DIFFRACTIONr_mcbond_other3.8563.9897483
X-RAY DIFFRACTIONr_mcangle_it5.7565.9629334
X-RAY DIFFRACTIONr_mcangle_other5.7555.9639335
X-RAY DIFFRACTIONr_scbond_it4.9084.6967781
X-RAY DIFFRACTIONr_scbond_other4.9074.6977782
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6876.76811273
X-RAY DIFFRACTIONr_long_range_B_refined10.73132.72617254
X-RAY DIFFRACTIONr_long_range_B_other10.73132.72917255
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 371 -
Rwork0.307 7519 -
obs--97.32 %

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