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- PDB-3do8: The crystal structure of the protein with unknown function from A... -

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Basic information

Entry
Database: PDB / ID: 3do8
TitleThe crystal structure of the protein with unknown function from Archaeoglobus fulgidus
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Protein with unknown function / Archaeoglobus fulgidus / Structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / Coenzyme A biosynthesis / Cytoplasm / Nucleotidyltransferase
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, archaea / 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
Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2008
Title: The crystal structure of the protein with unknown function from Archaeoglobus fulgidus
Authors: Zhang, R. / Wu, R. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJul 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,8262
Polymers33,8262
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-8 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.001, 63.781, 47.047
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein existed as dimer. The deposited Mol.A and Mol.B represent the dimer in the assymmetric unit.

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Components

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


Mass: 16912.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: coaD, AF_2206 / Plasmid: PDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O28077, pantetheine-phosphate adenylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, pH7.5, 30%PEG MME, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→47.89 Å / Num. all: 35569 / Num. obs: 34228 / % possible obs: 96.23 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 25.78
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.25 / Num. unique all: 2757 / % possible all: 86.87

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→47.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.255 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.092
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21372 1789 5 %RANDOM
Rwork0.16678 ---
obs0.16909 34228 96.23 %-
all-35569 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å2-0.51 Å2
2---0.18 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 216 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222126
X-RAY DIFFRACTIONr_bond_other_d0.0010.021557
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9832851
X-RAY DIFFRACTIONr_angle_other_deg0.98833776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01722.13589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42315430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.041523
X-RAY DIFFRACTIONr_chiral_restr0.0930.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
X-RAY DIFFRACTIONr_nbd_refined0.2340.2466
X-RAY DIFFRACTIONr_nbd_other0.2030.21675
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21050
X-RAY DIFFRACTIONr_nbtor_other0.080.21185
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.221
X-RAY DIFFRACTIONr_mcbond_it1.9171.51683
X-RAY DIFFRACTIONr_mcbond_other0.8211.5525
X-RAY DIFFRACTIONr_mcangle_it2.21722088
X-RAY DIFFRACTIONr_scbond_it3.7673976
X-RAY DIFFRACTIONr_scangle_it5.0554.5763
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 114 -
Rwork0.199 2281 -
obs-2395 86.87 %
Refinement TLS params.Method: refined / Origin x: 8.898 Å / Origin y: 12.035 Å / Origin z: 34.019 Å
111213212223313233
T-0.0145 Å20.0107 Å2-0.0138 Å2--0.0174 Å20.003 Å2---0.0411 Å2
L0.9462 °2-0.2316 °20.0078 °2-0.334 °20.0493 °2--0.064 °2
S-0.0534 Å °-0.0472 Å °-0.0463 Å °0.0223 Å °0.0403 Å °-0.0237 Å °-0.0095 Å °-0.0182 Å °0.0131 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1411 - 141
2X-RAY DIFFRACTION1BB2 - 1242 - 124

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