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- PDB-3nv7: Crystal structure of H.pylori phosphopantetheine adenylyltransfer... -

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Basic information

Entry
Database: PDB / ID: 3nv7
TitleCrystal structure of H.pylori phosphopantetheine adenylyltransferase mutant I4V/N76Y
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Helicobacter pylori 26695 strain / mutant I4V/N76Y / phosphopantetheine adenylyltransferase
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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChen, C.H. / Cheng, C.S. / Yin, H.S.
CitationJournal: To be Published
Title: Crystal structure of H.pylori phosphopantetheine adenylyltransferase mutant I4V/N76Y
Authors: Chen, C.H. / Cheng, C.S. / Yin, H.S.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1716
Polymers17,7271
Non-polymers4445
Water2,450136
1
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,68424
Polymers70,9064
Non-polymers1,77720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area17350 Å2
ΔGint-132 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.022, 69.459, 95.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

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Components

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


Mass: 17726.623 Da / Num. of mol.: 1 / Mutation: I4V, N76Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: coaD, kdtB, HP_1475 / Production host: Escherichia coli (E. coli)
References: UniProt: O26010, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 10% PEG 4000, 0.1M sodium acetate, 0.2M Li2SO4, pH 5.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 18626
Reflection shellResolution: 1.75→1.81 Å / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1T

1h1t


Resolution: 1.75→23.98 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.788 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 941 5.1 %RANDOM
Rwork0.1868 ---
obs0.1896 17485 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.82 Å2 / Biso mean: 31.2635 Å2 / Biso min: 16.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→23.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 24 136 1384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221270
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9841717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3055154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9723.72551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35915225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.274155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02919
X-RAY DIFFRACTIONr_nbd_refined0.2180.2561
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2881
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.222
X-RAY DIFFRACTIONr_mcbond_it1.5361.5798
X-RAY DIFFRACTIONr_mcangle_it2.44221252
X-RAY DIFFRACTIONr_scbond_it3.4523524
X-RAY DIFFRACTIONr_scangle_it4.8984.5465
LS refinement shellResolution: 1.749→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 60 -
Rwork0.248 1178 -
all-1238 -
obs--92.32 %

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