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- PDB-4jn5: Crystal structures of the first condensation domain of the CDA sy... -

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Basic information

Entry
Database: PDB / ID: 4jn5
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 / MOLECULAR REPLACEMENT / Resolution: 2.44 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 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,0692
Polymers97,0692
Non-polymers00
Water5,999333
1
A: CDA peptide synthetase I


Theoretical massNumber of molelcules
Total (without water)48,5341
Polymers48,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CDA peptide synthetase I


Theoretical massNumber of molelcules
Total (without water)48,5341
Polymers48,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.130, 82.438, 87.732
Angle α, β, γ (deg.)90.00, 106.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CDA peptide synthetase I


Mass: 48534.469 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.: 333 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 9-13% PEG 10000, 0.1 M HEPES, VAPOR DIFFUSION, SITTING DROP, temperature 277K
PH range: 7.1-7.3

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 31620

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→33.905 Å / SU ML: 0.36 / σ(F): 0.1 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 2028 6.63 %
Rwork0.1998 --
obs0.2036 30570 95.85 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.106 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1339 Å20 Å2-0.3569 Å2
2--3.4458 Å20 Å2
3----3.0259 Å2
Refinement stepCycle: LAST / Resolution: 2.44→33.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 0 333 6883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026695
X-RAY DIFFRACTIONf_angle_d0.4979118
X-RAY DIFFRACTIONf_dihedral_angle_d10.1342448
X-RAY DIFFRACTIONf_chiral_restr0.0331018
X-RAY DIFFRACTIONf_plane_restr0.0021216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.49720.36041360.28071825X-RAY DIFFRACTION87
2.4972-2.56470.35481410.25951944X-RAY DIFFRACTION92
2.5647-2.64020.32031190.25781934X-RAY DIFFRACTION91
2.6402-2.72540.34671530.24091971X-RAY DIFFRACTION93
2.7254-2.82270.30941470.23311967X-RAY DIFFRACTION94
2.8227-2.93570.2761410.21642050X-RAY DIFFRACTION96
2.9357-3.06920.26891410.20482022X-RAY DIFFRACTION96
3.0692-3.23090.23421400.20992090X-RAY DIFFRACTION97
3.2309-3.43310.28131540.20682093X-RAY DIFFRACTION98
3.4331-3.69790.25741410.19472085X-RAY DIFFRACTION98
3.6979-4.06950.21641540.17892105X-RAY DIFFRACTION99
4.0695-4.65710.211550.15652135X-RAY DIFFRACTION100
4.6571-5.86250.22941530.17932139X-RAY DIFFRACTION100
5.8625-33.90830.22231530.18642182X-RAY DIFFRACTION100

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