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- PDB-6kkw: Crystal structure of the complex of phosphopantetheine adenylyl t... -

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Basic information

Entry
Database: PDB / ID: 6kkw
TitleCrystal structure of the complex of phosphopantetheine adenylyl transferase from Acinetobacter baumannii with Dephospho Coenzyme at 3.2 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
DEPHOSPHO COENZYME A / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.202 Å
AuthorsViswanathan, V. / Gupta, A. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of phosphopantetheine adenylyl transferase from Acinetobacter baumannii with Dephospho Coenzyme at 3.2 A resolution.
Authors: Viswanathan, V. / Gupta, A. / Sharma, S. / Singh, T.P.
History
DepositionJul 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,2023
Polymers18,4791
Non-polymers7232
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-13 kcal/mol
Surface area9020 Å2
Unit cell
Length a, b, c (Å)215.539, 215.539, 215.539
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein Phosphopantetheine adenylyltransferase


Mass: 18479.033 Da / Num. of mol.: 1
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H35N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.64 Å3/Da / Density % sol: 78.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1M LITHIUM SULPHATE, 2M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→49.5 Å / Num. obs: 6957 / % possible obs: 92.27 % / Redundancy: 8.5 % / CC1/2: 0.98 / Rrim(I) all: 0.117 / Net I/σ(I): 30.61
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 13 % / Mean I/σ(I) obs: 5.02 / Num. unique obs: 534 / CC1/2: 0.92 / Rrim(I) all: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JOG

6jog


Resolution: 3.202→49.497 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.406 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.643 / ESU R Free: 0.354
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2327 334 4.801 %
Rwork0.175 6623 -
all0.178 --
obs-6957 92.378 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 76.279 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.202→49.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 45 22 1372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131381
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171266
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.6441874
X-RAY DIFFRACTIONr_angle_other_deg1.3171.572925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.415162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.54521.39279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.83315224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8351510
X-RAY DIFFRACTIONr_chiral_restr0.070.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021531
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02310
X-RAY DIFFRACTIONr_nbd_refined0.230.2336
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.21225
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2668
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.238
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.213
X-RAY DIFFRACTIONr_nbd_other0.30.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0750.21
X-RAY DIFFRACTIONr_mcbond_it7.4997.589651
X-RAY DIFFRACTIONr_mcbond_other7.4617.584650
X-RAY DIFFRACTIONr_mcangle_it11.48911.368812
X-RAY DIFFRACTIONr_mcangle_other11.48511.378813
X-RAY DIFFRACTIONr_scbond_it9.28.741730
X-RAY DIFFRACTIONr_scbond_other9.1948.749731
X-RAY DIFFRACTIONr_scangle_it13.6912.7411061
X-RAY DIFFRACTIONr_scangle_other13.68312.751062
X-RAY DIFFRACTIONr_lrange_it17.22291.6491554
X-RAY DIFFRACTIONr_lrange_other17.22591.7211552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.202-3.2850.67610.40913X-RAY DIFFRACTION2.5878
3.285-3.3750.281220.241472X-RAY DIFFRACTION93.5606
3.375-3.4730.32290.236481X-RAY DIFFRACTION100
3.473-3.5790.26200.21471X-RAY DIFFRACTION100
3.579-3.6970.287250.216461X-RAY DIFFRACTION100
3.697-3.8260.283220.191448X-RAY DIFFRACTION100
3.826-3.9710.164270.16423X-RAY DIFFRACTION100
3.971-4.1320.192180.154422X-RAY DIFFRACTION99.7732
4.132-4.3160.197170.143402X-RAY DIFFRACTION100
4.316-4.5260.143180.122378X-RAY DIFFRACTION100
4.526-4.7710.182210.113375X-RAY DIFFRACTION100
4.771-5.060.181150.134350X-RAY DIFFRACTION100
5.06-5.4090.31490.151340X-RAY DIFFRACTION100
5.409-5.8410.228170.178316X-RAY DIFFRACTION100
5.841-6.3970.266150.191289X-RAY DIFFRACTION100
6.397-7.150.311130.201262X-RAY DIFFRACTION100
7.15-8.2510.265180.194238X-RAY DIFFRACTION100
8.251-10.0950.223110.143211X-RAY DIFFRACTION100
10.095-14.2290.176130.183160X-RAY DIFFRACTION98.2955
14.229-49.4970.82530.48111X-RAY DIFFRACTION92.6829

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