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- PDB-4jn3: Crystal structures of the first condensation domain of the CDA sy... -

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Basic information

Entry
Database: PDB / ID: 4jn3
TitleCrystal structures of the first condensation domain of the CDA synthetase
ComponentsCDA peptide synthetase I
KeywordsBIOSYNTHETIC PROTEIN / nonribosomal peptide synthetase / NRPS condensation domain / calcium-dependent antibiotic / peptide bond formation / CoA dependant acyltransferase superfamily
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / organic cyclic compound biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity
Similarity search - Function
Nonribosomal peptide synthetase, condensation domain / Non-ribosomal peptide synthase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Nonribosomal peptide synthetase, condensation domain / Non-ribosomal peptide synthase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CDA peptide synthetase I
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.69 Å
AuthorsBloudoff, K. / Schmeing, T.M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal Structures of the First Condensation Domain of CDA Synthetase Suggest Conformational Changes during the Synthetic Cycle of Nonribosomal Peptide Synthetases.
Authors: Bloudoff, K. / Rodionov, D. / Schmeing, T.M.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDA peptide synthetase I
B: CDA peptide synthetase I


Theoretical massNumber of molelcules
Total (without water)97,8192
Polymers97,8192
Non-polymers00
Water22,9691275
1
A: CDA peptide synthetase I


Theoretical massNumber of molelcules
Total (without water)48,9101
Polymers48,9101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CDA peptide synthetase I


Theoretical massNumber of molelcules
Total (without water)48,9101
Polymers48,9101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.789, 83.479, 177.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CDA peptide synthetase I


Mass: 48909.625 Da / Num. of mol.: 2 / Fragment: first condensation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO3230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z4X6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1275 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25-27% PEG 3000, 0.2-0.25M lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97860, 0.9792, 0.9070
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97921
30.9071
ReflectionResolution: 1.69→50 Å / Num. obs: 100050

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AutoSolphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.69→34.112 Å / SU ML: 0.2 / σ(F): 0.21 / Phase error: 21.89 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.212 2000 2 %
Rwork0.1924 --
obs0.1928 100050 95.58 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.161 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2304 Å20 Å2-0 Å2
2--0.2806 Å20 Å2
3----4.511 Å2
Refinement stepCycle: LAST / Resolution: 1.69→34.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6784 0 0 1275 8059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046938
X-RAY DIFFRACTIONf_angle_d0.8219452
X-RAY DIFFRACTIONf_dihedral_angle_d11.0922546
X-RAY DIFFRACTIONf_chiral_restr0.0521048
X-RAY DIFFRACTIONf_plane_restr0.0031268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.73520.37361210.32635947X-RAY DIFFRACTION82
1.7352-1.78210.34021330.29566492X-RAY DIFFRACTION90
1.7821-1.83460.28391360.2666651X-RAY DIFFRACTION92
1.8346-1.89380.27871370.23736753X-RAY DIFFRACTION93
1.8938-1.96140.28081410.2216926X-RAY DIFFRACTION95
1.9614-2.040.23221440.20527039X-RAY DIFFRACTION97
2.04-2.13280.2221450.19487107X-RAY DIFFRACTION98
2.1328-2.24520.22251460.19027168X-RAY DIFFRACTION98
2.2452-2.38590.22011450.18597123X-RAY DIFFRACTION98
2.3859-2.570.2141470.18657169X-RAY DIFFRACTION98
2.57-2.82850.20541480.1847257X-RAY DIFFRACTION99
2.8285-3.23750.18691480.18597304X-RAY DIFFRACTION99
3.2375-4.07790.19041520.1677422X-RAY DIFFRACTION100
4.0779-34.11930.16871570.17357692X-RAY DIFFRACTION99

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