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- PDB-5h16: Crystal structure of the complex of Phosphopantetheine adenylyltr... -

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Basic information

Entry
Database: PDB / ID: 5h16
TitleCrystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with citrate at 2.3 A resolution.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE
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
CITRIC ACID / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGupta, A. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii at 2.3 A resolution.
Authors: Gupta, A. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,02712
Polymers110,8746
Non-polymers1,1536
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17210 Å2
ΔGint-90 kcal/mol
Surface area39290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.590, 109.813, 121.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLYAA3 - 1623 - 162
21LYSLYSGLYGLYBB3 - 1623 - 162
12LYSLYSGLYGLYAA3 - 1623 - 162
22LYSLYSGLYGLYCC3 - 1623 - 162
13LYSLYSGLYGLYAA3 - 1623 - 162
23LYSLYSGLYGLYDD3 - 1623 - 162
14METMETTRPTRPAA1 - 1631 - 163
24METMETTRPTRPEE1 - 1631 - 163
15METMETTRPTRPAA1 - 1631 - 163
25METMETTRPTRPFF1 - 1631 - 163
16LYSLYSTRPTRPBB3 - 1633 - 163
26LYSLYSTRPTRPCC3 - 1633 - 163
17LYSLYSTRPTRPBB3 - 1633 - 163
27LYSLYSTRPTRPDD3 - 1633 - 163
18LYSLYSGLYGLYBB3 - 1623 - 162
28LYSLYSGLYGLYEE3 - 1623 - 162
19LYSLYSGLYGLYBB3 - 1623 - 162
29LYSLYSGLYGLYFF3 - 1623 - 162
110LYSLYSTRPTRPCC3 - 1633 - 163
210LYSLYSTRPTRPDD3 - 1633 - 163
111LYSLYSGLYGLYCC3 - 1623 - 162
211LYSLYSGLYGLYEE3 - 1623 - 162
112LYSLYSGLYGLYCC3 - 1623 - 162
212LYSLYSGLYGLYFF3 - 1623 - 162
113LYSLYSGLYGLYDD3 - 1623 - 162
213LYSLYSGLYGLYEE3 - 1623 - 162
114LYSLYSGLYGLYDD3 - 1623 - 162
214LYSLYSGLYGLYFF3 - 1623 - 162
115METMETTRPTRPEE1 - 1631 - 163
215METMETTRPTRPFF1 - 1631 - 163

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 18479.033 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: coaD / Production host: Escherichia coli (E. coli)
References: UniProt: A0A059ZFC5, UniProt: B0VTH7*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES Na pH 7.5, 1.0M Na citrate tribasic dihydrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 28, 2016 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→81.56 Å / Num. obs: 46855 / % possible obs: 99.2 % / Redundancy: 3.3 % / Rsym value: 0.15 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 0.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1T

1h1t


Resolution: 2.3→81.56 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.857 / SU B: 11.071 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.464 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30226 949 2 %RANDOM
Rwork0.26132 ---
obs0.26212 45713 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.788 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0 Å2-0 Å2
2---0.46 Å20 Å2
3---1.62 Å2
Refinement stepCycle: 1 / Resolution: 2.3→81.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7788 0 78 124 7990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198040
X-RAY DIFFRACTIONr_bond_other_d0.0020.027659
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.94410878
X-RAY DIFFRACTIONr_angle_other_deg1.081317523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25423.433402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.135151332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7841560
X-RAY DIFFRACTIONr_chiral_restr0.1790.21206
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022010
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2823.5523882
X-RAY DIFFRACTIONr_mcbond_other3.2813.5513881
X-RAY DIFFRACTIONr_mcangle_it5.2755.3134842
X-RAY DIFFRACTIONr_mcangle_other5.2755.3134843
X-RAY DIFFRACTIONr_scbond_it3.614.154158
X-RAY DIFFRACTIONr_scbond_other3.614.154156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8776.0246036
X-RAY DIFFRACTIONr_long_range_B_refined10.18767.7632819
X-RAY DIFFRACTIONr_long_range_B_other10.18967.75532808
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A102820.09
12B102820.09
21A100940.1
22C100940.1
31A102040.1
32D102040.1
41A104440.09
42E104440.09
51A102760.1
52F102760.1
61B102940.1
62C102940.1
71B103020.1
72D103020.1
81B103080.08
82E103080.08
91B101720.1
92F101720.1
101C101580.11
102D101580.11
111C101440.09
112E101440.09
121C101660.1
122F101660.1
131D101420.11
132E101420.11
141D100580.11
142F100580.11
151E103140.1
152F103140.1
LS refinement shellResolution: 2.305→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 64 -
Rwork0.332 3276 -
obs--96.73 %

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