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- PDB-3wdl: Crystal structure of 4-phosphopantoate-beta-alanine ligase comple... -

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Basic information

Entry
Database: PDB / ID: 3wdl
TitleCrystal structure of 4-phosphopantoate-beta-alanine ligase complexed with ATP
Components4-phosphopantoate--beta-alanine ligase
KeywordsLIGASE
Function / homology
Function and homology information


4-phosphopantoate-beta-alanine ligase / acid-amino acid ligase activity / coenzyme A biosynthetic process / ATP binding
Similarity search - Function
Phosphopantoate/pantothenate synthetase / Phosphopantoate/pantothenate synthetase / Phosphopantoate/pantothenate synthetase superfamily / Phosphopantothenate/pantothenate synthetase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 4-phosphopantoate--beta-alanine ligase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKishimoto, A. / Kita, A. / Ishibashi, T. / Tomita, H. / Yokooji, Y. / Imanaka, T. / Atomi, H. / Miki, K.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis
Authors: Kishimoto, A. / Kita, A. / Ishibashi, T. / Tomita, H. / Yokooji, Y. / Imanaka, T. / Atomi, H. / Miki, K.
History
DepositionJun 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: 4-phosphopantoate--beta-alanine ligase
B: 4-phosphopantoate--beta-alanine ligase
C: 4-phosphopantoate--beta-alanine ligase
D: 4-phosphopantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,64410
Polymers119,5664
Non-polymers2,0776
Water1,51384
1
A: 4-phosphopantoate--beta-alanine ligase
B: 4-phosphopantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8225
Polymers59,7832
Non-polymers1,0393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-37 kcal/mol
Surface area21000 Å2
MethodPISA
2
C: 4-phosphopantoate--beta-alanine ligase
D: 4-phosphopantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8225
Polymers59,7832
Non-polymers1,0393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-36 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.655, 80.071, 83.998
Angle α, β, γ (deg.)90.00, 110.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-phosphopantoate--beta-alanine ligase / Phosphopantothenate synthetase / PPS


Mass: 29891.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1686 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JIZ8, 4-phosphopantoate-beta-alanine ligase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 17% PEG 10000, 100mM ammonium acetate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 21, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 38007 / Num. obs: 38007 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2
Reflection shellResolution: 2.4→2.44 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1549101.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1881 5 %RANDOM
Rwork0.227 ---
obs0.227 37989 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.9503 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--9.68 Å20 Å27.25 Å2
2--11.55 Å20 Å2
3----1.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7734 0 126 84 7944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d1.98
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 291 4.8 %
Rwork0.281 5732 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4atp_cns37.paramatp_cns.top

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