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- PDB-1od6: The Crystal Structure of Phosphopantetheine adenylyltransferase f... -

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Basic information

Entry
Database: PDB / ID: 1od6
TitleThe Crystal Structure of Phosphopantetheine adenylyltransferase from Thermus Thermophilus in complex with 4'-phosphopantetheine
ComponentsPHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / COENZYME A BIOSYNTHESIS / NUCLEOTIDYLTRANSFERASE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
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
4'-PHOSPHOPANTETHEINE / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTakahashi, H. / Inagaki, E. / Miyano, M. / Tahirov, T.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure and Implications for the Thermal Stability of Phosphopantetheine Adenylyltransferase from Thermus Thermophilus.
Authors: Takahashi, H. / Inagaki, E. / Fujimoto, Y. / Kuroishi, C. / Nodake, Y. / Nakamura, Y. / Arisaka, F. / Yutani, K. / Kuramitsu, S. / Yokoyama, S. / Yamamoto, M. / Miyano, M. / Tahirov, T.H.
History
DepositionFeb 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2003Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3775
Polymers17,7301
Non-polymers6474
Water2,918162
1
A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)110,26230
Polymers106,3836
Non-polymers3,87924
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation18_654-x+4/3,-x+y+2/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
Buried area22500 Å2
ΔGint-485.5 kcal/mol
Surface area33610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.715, 115.715, 115.661
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

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Components

#1: Protein PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE / PPAT


Mass: 17730.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET 11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5SJS9, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 4.2 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.3
Details: PROTEIN WAS CRYSTALLIZED FROM 1.1M LISULF, 100 MM MES, PH 6.25.
Crystal grow
*PLUS
Temperature: 291 K / pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.13 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
30.2 M1dropNaCl
41.1 M1reservoirLi2SO4
50.1 Msodium MES1reservoirpH6.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 47654 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 8 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. measured all: 334505 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

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

1qjc


Resolution: 1.5→37.8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1745265.87 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.201 4761 10.1 %RANDOM
Rwork0.196 ---
obs0.196 47263 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0.02 Å20 Å2
2---1.27 Å20 Å2
3---2.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.5→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 37 162 1408
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.741.5
X-RAY DIFFRACTIONc_mcangle_it3.932
X-RAY DIFFRACTIONc_scbond_it4.652
X-RAY DIFFRACTIONc_scangle_it6.652.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 750 9.7 %
Rwork0.319 6974 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3LIGAND.PARLIGAND.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.2005 / Rfactor Rwork: 0.1962
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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