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- PDB-7ed2: Transferase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 7ed2
TitleTransferase from Mycobacterium smegmatis
Components4'-phosphopantetheinyl transferase
KeywordsTRANSFERASE / phosphopantetheine transferase
Function / homologyADENOSINE-3'-5'-DIPHOSPHATE / 4'-phosphopantetheinyl transferase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKim, D.-G. / Lee, B.-J. / Lee, S.J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2018R1A2A1A19018526 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2018R1A5A2024425 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1F1A1075828 Korea, Republic Of
CitationJournal: To Be Published
Title: Transferase from Mycobacterium tuberculosis
Authors: Kim, D.-G. / Lee, B.-J. / Lee, S.J.
History
DepositionMar 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Aug 14, 2024Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_contact_author ...entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _struct.title ..._entity_src_gen.gene_src_common_name / _struct.title / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4'-phosphopantetheinyl transferase
B: 4'-phosphopantetheinyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0488
Polymers50,0972
Non-polymers9526
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.410, 78.603, 81.869
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 4'-phosphopantetheinyl transferase


Mass: 25048.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: ERS451418_02655 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAI9EXQ5
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris, pH 8.5, 250 mM magnesium chloride, 40% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 52709 / % possible obs: 99.2 % / Redundancy: 4 % / CC1/2: 0.995 / Net I/σ(I): 29.15
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 2609 / CC1/2: 0.668

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→28.37 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.548 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 2682 5.1 %RANDOM
Rwork0.1817 ---
obs0.1836 49918 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.47 Å2 / Biso mean: 28.298 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.65→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 58 157 3601
Biso mean--21.85 32 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173308
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.6444836
X-RAY DIFFRACTIONr_angle_other_deg1.3941.5767626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.94320.11182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4451534
X-RAY DIFFRACTIONr_chiral_restr0.0780.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 194 -
Rwork0.325 3658 -
all-3852 -
obs--99.69 %

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