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- PDB-5z1m: Crystal structure of the complex of trimeric Phosphopantetheine a... -

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Basic information

Entry
Database: PDB / ID: 5z1m
TitleCrystal structure of the complex of trimeric Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with citrate ion at 1.87 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: 1.87 Å
AuthorsSingh, P.K. / Gupta, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of trimeric Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with citrate ion at 1.87 A resolution
Authors: Singh, P.K. / Gupta, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0136
Polymers55,4373
Non-polymers5763
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-19 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.250, 118.820, 109.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 1 - 163 / Label seq-ID: 1 - 163

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 18479.033 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
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: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2017 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.87→41.6 Å / Num. obs: 41511 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 20.8
Reflection shellResolution: 1.87→1.897 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2056 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H7X

5h7x


Resolution: 1.87→41.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.806 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 2052 4.9 %RANDOM
Rwork0.18555 ---
obs0.18802 39459 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.637 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å2-0 Å2
2--2.41 Å20 Å2
3----1.8 Å2
Refinement stepCycle: 1 / Resolution: 1.87→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 39 202 4156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194041
X-RAY DIFFRACTIONr_bond_other_d0.0020.023729
X-RAY DIFFRACTIONr_angle_refined_deg2.3291.9455466
X-RAY DIFFRACTIONr_angle_other_deg1.1938610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93923.433201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03615672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8941530
X-RAY DIFFRACTIONr_chiral_restr0.2350.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
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_it2.6032.71953
X-RAY DIFFRACTIONr_mcbond_other2.6032.6981952
X-RAY DIFFRACTIONr_mcangle_it3.7074.0282436
X-RAY DIFFRACTIONr_mcangle_other3.7074.032437
X-RAY DIFFRACTIONr_scbond_it3.4773.262088
X-RAY DIFFRACTIONr_scbond_other3.4763.2592086
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2344.7073030
X-RAY DIFFRACTIONr_long_range_B_refined7.83752.82616692
X-RAY DIFFRACTIONr_long_range_B_other7.81252.65316633
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)
11A104520.09
12B104520.09
21A104280.1
22C104280.1
31B104240.09
32C104240.09
LS refinement shellResolution: 1.865→1.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 155 -
Rwork0.302 2897 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.47221.31441.58312.70180.8562.08820.08070.1299-0.0324-0.1454-0.0675-0.0478-0.0558-0.1355-0.01320.03660.05060.01620.1571-0.03160.087915.1427-27.843924.6805
22.3528-1.29720.65582.4806-0.3263.13580.0560.34730.0365-0.1755-0.02210.1024-0.0233-0.0813-0.03390.084-0.02050.03430.16090.04890.068642.3352-19.22168.0853
32.45940.3184-0.61732.0172-0.08943.82070.12380.26420.0764-0.5120.10130.21260.0904-0.0914-0.22510.33030.0165-0.11280.0367-0.00550.123535.2077-51.045912.5923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 163
2X-RAY DIFFRACTION2B1 - 163
3X-RAY DIFFRACTION3C1 - 163

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