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- PDB-4r0n: Hexagonal form of phosphopantetheine adenylyltransferase from Myc... -

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Basic information

Entry
Database: PDB / ID: 4r0n
TitleHexagonal form of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Nucleotidyltransferase
Function / homologyHUPs / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Function and homology information
Biological speciesMycobacterium tuberculosis BT1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTimofeev, V.I. / Smirnova, E.A. / Chupova, L.A. / Esipov, R.S. / Kuranova, I.P.
CitationJournal: TO BE PUBLISHED
Title: Hexagonal form of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis
Authors: Timofeev, V.I. / Smirnova, E.A. / Chupova, L.A. / Esipov, R.S. / Kuranova, I.P.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal_grow / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.method / _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: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
G: Phosphopantetheine adenylyltransferase
I: Phosphopantetheine adenylyltransferase
K: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,94014
Polymers102,1716
Non-polymers7698
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-215 kcal/mol
Surface area36900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.472, 106.472, 71.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 17028.543 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis BT1 (bacteria)
Gene: coaD, HKBT1_3114 / Production host: Escherichia coli (E. coli)
References: UniProt: W6HGL0, UniProt: A0A7U4DCE7*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growMethod: counter-diffusion / Details: Counter diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 57597 / % possible obs: 94.31 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E1A

4e1a


Resolution: 2→19.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.194 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26554 2916 5.1 %RANDOM
Rwork0.20986 ---
obs0.21264 54681 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7158 0 40 263 7461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197310
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9699903
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68623.396318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.556151191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4091560
X-RAY DIFFRACTIONr_chiral_restr0.0920.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215478
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 188 -
Rwork0.359 3697 -
obs--87.9 %
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)
11.90280.9524-0.93172.8467-0.90740.9936-0.13740.2183-0.1079-0.40350.0404-0.31210.153-0.03540.0970.12510.00980.02260.0805-0.01940.0434-2.764613.844-3.9186
21.8857-0.5910.53033.2701-0.28530.57960.10650.197-0.1681-0.3092-0.04850.22890.108-0.0122-0.05790.0846-0.0043-0.020.1273-0.02750.0271-36.37919.0096-6.1251
31.9722-0.91970.75412.4701-0.96640.9834-0.1256-0.22280.1460.39630.0313-0.3334-0.1848-0.01730.09430.1299-0.0095-0.03890.0877-0.01780.0512-2.763747.59210.7621
42.45440.51470.1031.4477-0.7741.1572-0.0359-0.4050.00580.23880.09290.092-0.1103-0.176-0.0570.11760.0192-0.00090.1260.01170.011-14.34918.479123.679
51.28560.5057-0.36543.1673-0.26490.48610.0852-0.19610.16670.3041-0.05870.2508-0.0929-0.0208-0.02650.08450.00490.02120.1404-0.02750.0355-36.382642.442112.9819
63.3553-0.3255-0.12511.3868-0.61260.81970.00030.4543-0.0133-0.26760.06460.06870.0982-0.1452-0.0650.1208-0.0156-0.00550.12890.00510.0065-14.353942.9695-16.8361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 157
2X-RAY DIFFRACTION2C2 - 157
3X-RAY DIFFRACTION3E2 - 157
4X-RAY DIFFRACTION4G2 - 157
5X-RAY DIFFRACTION5I2 - 157
6X-RAY DIFFRACTION6K2 - 157

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