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- PDB-5h7x: Crystal structure of the complex of Phosphopantetheine adenylyltr... -

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Basic information

Entry
Database: PDB / ID: 5h7x
TitleCrystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with 2-hydroxy-1,2,3-propane tricarboxylate at 1.76 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: 1.76 Å
AuthorsSingh, P.K. / Gupta, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii.
Authors: Gupta, A. / Singh, P.K. / Iqbal, N. / Sharma, P. / Baraigya, H.R. / Kaur, P. / Umar, M.S. / Ahmad, F. / Sharma, A. / Owais, M. / Sharma, S. / Singh, T.P.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_prerelease_seq
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)116,86312
Polymers115,7106
Non-polymers1,1536
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17660 Å2
ΔGint-83 kcal/mol
Surface area40580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.262, 109.389, 121.275
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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTRPTRPAA1 - 1639 - 171
21METMETTRPTRPBB1 - 1639 - 171
12METMETTRPTRPAA1 - 1639 - 171
22METMETTRPTRPCC1 - 1639 - 171
13METMETTRPTRPAA1 - 1639 - 171
23METMETTRPTRPDD1 - 1639 - 171
14METMETGLYGLYAA1 - 1629 - 170
24METMETGLYGLYEE1 - 1629 - 170
15METMETGLYGLYAA1 - 1629 - 170
25METMETGLYGLYFF1 - 1629 - 170
16METMETTRPTRPBB1 - 1639 - 171
26METMETTRPTRPCC1 - 1639 - 171
17METMETTRPTRPBB1 - 1639 - 171
27METMETTRPTRPDD1 - 1639 - 171
18METMETGLYGLYBB1 - 1629 - 170
28METMETGLYGLYEE1 - 1629 - 170
19METMETGLYGLYBB1 - 1629 - 170
29METMETGLYGLYFF1 - 1629 - 170
110METMETTRPTRPCC1 - 1639 - 171
210METMETTRPTRPDD1 - 1639 - 171
111METMETGLYGLYCC1 - 1629 - 170
211METMETGLYGLYEE1 - 1629 - 170
112METMETGLYGLYCC1 - 1629 - 170
212METMETGLYGLYFF1 - 1629 - 170
113METMETGLYGLYDD1 - 1629 - 170
213METMETGLYGLYEE1 - 1629 - 170
114METMETGLYGLYDD1 - 1629 - 170
214METMETGLYGLYFF1 - 1629 - 170
115GLYGLYTRPTRPEE-7 - 1631 - 171
215GLYGLYTRPTRPFF-7 - 1631 - 171

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: 19284.963 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: B0V8I3*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.3 Å3/Da / Density % sol: 47.6 %
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: Sep 22, 2016 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.76→40.61 Å / Num. obs: 103655 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rsym value: 0.138 / Net I/σ(I): 10.5
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.2 % / % possible all: 95.5

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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: 1.76→40.61 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.37 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.132 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25634 1118 1.1 %RANDOM
Rwork0.20928 ---
obs0.20978 102125 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.32 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.76→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7944 0 78 631 8653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198200
X-RAY DIFFRACTIONr_bond_other_d0.0030.027814
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.94511092
X-RAY DIFFRACTIONr_angle_other_deg1.045317882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39323.35406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.748151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.861562
X-RAY DIFFRACTIONr_chiral_restr0.2130.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029292
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022046
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_it3.7783.613970
X-RAY DIFFRACTIONr_mcbond_other3.7723.6093969
X-RAY DIFFRACTIONr_mcangle_it5.7865.3874952
X-RAY DIFFRACTIONr_mcangle_other5.7875.3884953
X-RAY DIFFRACTIONr_scbond_it4.7974.2974230
X-RAY DIFFRACTIONr_scbond_other4.7974.2974228
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3966.1956140
X-RAY DIFFRACTIONr_long_range_B_refined10.85768.99734124
X-RAY DIFFRACTIONr_long_range_B_other10.8668.98334096
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)
11A104160.11
12B104160.11
21A103140.12
22C103140.12
31A104540.1
32D104540.1
41A102400.11
42E102400.11
51A101940.11
52F101940.11
61B104700.09
62C104700.09
71B105620.09
72D105620.09
81B104140.08
82E104140.08
91B103640.08
92F103640.08
101C104140.11
102D104140.11
111C102700.1
112E102700.1
121C102900.09
122F102900.09
131D103320.11
132E103320.11
141D102660.1
142F102660.1
151E108300.09
152F108300.09
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 89 -
Rwork0.421 7205 -
obs--96.3 %

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