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- PDB-3l93: Phosphopantetheine adenylyltransferase from Yersinia pestis. -

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Basic information

Entry
Database: PDB / ID: 3l93
TitlePhosphopantetheine adenylyltransferase from Yersinia pestis.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / structural genomics / phosphopantetheine adenylyltransferase / ATP-binding / Coenzyme A biosynthesis / Nucleotide-binding / Nucleotidyltransferase / Center for Structural Genomics of Infectious Diseases / CSGID
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
FORMIC ACID / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsOsipiuk, J. / Maltseva, N. / Makowska-grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of phosphopantetheine adenylyltransferase from Yersinia pestis.
Authors: Osipiuk, J. / Maltseva, N. / Makowska-grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 1, 2014Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)17,9942
Polymers17,9481
Non-polymers461
Water1,42379
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)107,96412
Polymers107,6886
Non-polymers2766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area17220 Å2
ΔGint-150 kcal/mol
Surface area37910 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9826
Polymers53,8443
Non-polymers1383
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4320 Å2
ΔGint-38 kcal/mol
Surface area23250 Å2
MethodPISA
3
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9884
Polymers35,8962
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2920 Å2
ΔGint-24 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.511, 115.511, 117.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 17948.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: coaD, kdtB, y0088, YPO0053, YP_0054 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZJN9, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% Tacsimate, pH 7.0, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.16→32.3 Å / Num. all: 16233 / Num. obs: 16233 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.875 / Net I/σ(I): 15.7
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.88 / Num. unique all: 807 / Χ2: 1.484 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L92

3l92


Resolution: 2.16→32.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.388 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.146 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 812 5 %RANDOM
Rwork0.175 ---
all0.177 16216 --
obs0.177 16216 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.86 Å2 / Biso mean: 34.293 Å2 / Biso min: 19.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0.62 Å20 Å2
2---1.23 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.16→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 3 79 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221365
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9791865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4275186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96123.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31515258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.781157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211008
X-RAY DIFFRACTIONr_mcbond_it1.021.5849
X-RAY DIFFRACTIONr_mcangle_it1.85721388
X-RAY DIFFRACTIONr_scbond_it2.8473516
X-RAY DIFFRACTIONr_scangle_it4.5374.5464
LS refinement shellResolution: 2.161→2.217 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 61 -
Rwork0.252 1100 -
all-1161 -
obs-1161 96.51 %
Refinement TLS params.Method: refined / Origin x: 4.7938 Å / Origin y: 19.034 Å / Origin z: 45.1136 Å
111213212223313233
T0.149 Å2-0.0193 Å2-0.0006 Å2-0.0038 Å20.0047 Å2--0.0794 Å2
L2.7954 °2-0.4041 °20.5806 °2-1.7791 °2-1.2702 °2--1.9463 °2
S0.0148 Å °-0.0432 Å °-0.0823 Å °-0.171 Å °0.0469 Å °-0.1115 Å °0.0494 Å °-0.0311 Å °-0.0617 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 159
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A160 - 238

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