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- PDB-5dlk: The crystal structure of CT mutant -

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Basic information

Entry
Database: PDB / ID: 5dlk
TitleThe crystal structure of CT mutant
ComponentsTqaA
KeywordsUNKNOWN FUNCTION / Biochemistry / mutant
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / cytoplasm
Similarity search - Function
Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain ...Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Biological speciesPenicillium aethiopicum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, J.R. / Tang, Y. / Zhou, J.H.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural basis of nonribosomal peptide macrocyclization in fungi
Authors: Zhang, J. / Liu, N. / Cacho, R.A. / Gong, Z. / Liu, Z. / Qin, W. / Tang, C. / Tang, Y. / Zhou, J.
History
DepositionSep 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TqaA
B: TqaA
C: TqaA
D: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,42530
Polymers214,6824
Non-polymers1,74226
Water25,1311395
1
A: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1999
Polymers53,6711
Non-polymers5298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1999
Polymers53,6711
Non-polymers5298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0757
Polymers53,6711
Non-polymers4056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9515
Polymers53,6711
Non-polymers2804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.640, 221.678, 99.780
Angle α, β, γ (deg.)90.00, 127.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-663-

HOH

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Components

#1: Protein
TqaA


Mass: 53670.582 Da / Num. of mol.: 4 / Fragment: UNP residues 3595-4074 / Mutation: residues 3992-4001 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium aethiopicum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F1CWE4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1395 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Sodium malnate, Bis-Tris propane, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 256485 / % possible obs: 99.9 % / Redundancy: 5.6 % / Net I/σ(I): 22.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DIJ

5dij


Resolution: 1.8→41.906 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 12863 5.02 %
Rwork0.1929 --
obs0.1944 256012 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→41.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14083 0 104 1395 15582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714606
X-RAY DIFFRACTIONf_angle_d1.09619917
X-RAY DIFFRACTIONf_dihedral_angle_d13.715254
X-RAY DIFFRACTIONf_chiral_restr0.0462259
X-RAY DIFFRACTIONf_plane_restr0.0062557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-1.82030.31364380.29077850X-RAY DIFFRACTION97
1.8203-1.84170.32844570.27898092X-RAY DIFFRACTION100
1.8417-1.86420.29274230.26578103X-RAY DIFFRACTION100
1.8642-1.88780.25544210.25178147X-RAY DIFFRACTION100
1.8878-1.91260.29074220.2568182X-RAY DIFFRACTION100
1.9126-1.93880.29254320.25178017X-RAY DIFFRACTION100
1.9388-1.96650.24274080.22898131X-RAY DIFFRACTION100
1.9665-1.99590.24154350.22428120X-RAY DIFFRACTION100
1.9959-2.02710.2414340.22818104X-RAY DIFFRACTION100
2.0271-2.06030.25234600.22258035X-RAY DIFFRACTION100
2.0603-2.09580.27234400.22588100X-RAY DIFFRACTION100
2.0958-2.13390.26464350.21488082X-RAY DIFFRACTION100
2.1339-2.1750.24784190.21238164X-RAY DIFFRACTION100
2.175-2.21940.25544210.21048109X-RAY DIFFRACTION100
2.2194-2.26760.2654230.22618093X-RAY DIFFRACTION100
2.2676-2.32040.23764630.20648118X-RAY DIFFRACTION100
2.3204-2.37840.2364140.2078100X-RAY DIFFRACTION100
2.3784-2.44270.24814560.20548039X-RAY DIFFRACTION100
2.4427-2.51450.25813920.20428140X-RAY DIFFRACTION100
2.5145-2.59570.2494580.21048162X-RAY DIFFRACTION100
2.5957-2.68850.23784150.20298091X-RAY DIFFRACTION100
2.6885-2.79610.25234410.2038120X-RAY DIFFRACTION100
2.7961-2.92330.22624420.19948134X-RAY DIFFRACTION100
2.9233-3.07740.25214300.21478124X-RAY DIFFRACTION100
3.0774-3.27010.21644200.20478114X-RAY DIFFRACTION100
3.2701-3.52250.21314520.18898131X-RAY DIFFRACTION100
3.5225-3.87670.18134310.17388106X-RAY DIFFRACTION100
3.8767-4.43720.17683780.15078161X-RAY DIFFRACTION100
4.4372-5.58830.17783920.14518198X-RAY DIFFRACTION100
5.5883-41.91690.16534110.15048082X-RAY DIFFRACTION98

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