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- PDB-5du9: First condensation domain of the calcium-dependent antibiotic syn... -

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Basic information

Entry
Database: PDB / ID: 5du9
TitleFirst condensation domain of the calcium-dependent antibiotic synthetase in complex with substrate analogue 2a
ComponentsCDA peptide synthetase I
KeywordsPhosphopantetheine binding protein / Nonribosomal peptide synthetase / condensation domain / chemical probe / substrate analogue
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
(2S)-2-amino-N-butyl-propanamide / CDA peptide synthetase I
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsBloudoff, K. / Alonzo, D.A. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106615 Canada
CitationJournal: Cell Chem Biol / Year: 2016
Title: Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.
Authors: Bloudoff, K. / Alonzo, D.A. / Schmeing, T.M.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4727
Polymers97,0172
Non-polymers4555
Water22,8971271
1
A: CDA peptide synthetase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7844
Polymers48,5091
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CDA peptide synthetase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6883
Polymers48,5091
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)213.428, 213.428, 52.901
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein CDA peptide synthetase I


Mass: 48508.500 Da / Num. of mol.: 2 / Fragment: UNP residues1-449 / Mutation: E17C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO3230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z4X6
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-UM2 / (2S)-2-amino-N-butyl-propanamide / N-butyl-L-alaninamide


Type: L-peptide linking / Mass: 144.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1271 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25-27% PEG 3000, 0.2-0.25M Lithium Sulfate, 0.1 M HEPES, pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.53→42.17 Å / Num. obs: 135546 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 3.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.6→42.17 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1926 1656 1.4 %
Rwork0.1711 --
obs0.1714 118454 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 27 1271 7750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036662
X-RAY DIFFRACTIONf_angle_d0.8399089
X-RAY DIFFRACTIONf_dihedral_angle_d11.0652413
X-RAY DIFFRACTIONf_chiral_restr0.031022
X-RAY DIFFRACTIONf_plane_restr0.0041207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64710.27331360.2519707X-RAY DIFFRACTION100
1.6471-1.70030.25051380.23599749X-RAY DIFFRACTION100
1.7003-1.7610.26091380.22349738X-RAY DIFFRACTION100
1.761-1.83150.28331370.21749746X-RAY DIFFRACTION100
1.8315-1.91490.22471390.19799739X-RAY DIFFRACTION100
1.9149-2.01580.18711390.18799717X-RAY DIFFRACTION100
2.0158-2.14210.21691380.17349717X-RAY DIFFRACTION100
2.1421-2.30750.18511360.16219744X-RAY DIFFRACTION100
2.3075-2.53970.17661380.169759X-RAY DIFFRACTION100
2.5397-2.90710.20251370.16579750X-RAY DIFFRACTION100
2.9071-3.66240.18681380.15899735X-RAY DIFFRACTION100
3.6624-42.170.15811420.15199697X-RAY DIFFRACTION100
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)
12.66430.780.40092.93310.50061.8922-0.22390.20230.2994-0.32090.1845-0.0326-0.322-0.13510.04590.22760.0231-0.02440.17970.02980.07917.4078-7.26532.0286
21.3563-0.17220.61311.3444-0.13291.6427-0.0474-0.12520.05640.07350.03460.03220.0443-0.24390.00720.13830.00560.03660.1645-0.01240.061222.7932-25.464317.1569
30.54920.89-1.07244.3299-1.0522.3598-0.0177-0.11910.52080.01150.0389-0.38170.00470.2054-0.02330.0693-0.0056-0.02320.1907-0.04740.653767.2034-25.351625.3871
41.4191-0.052-0.62192.8917-0.66161.73230.0408-0.04720.77160.0436-0.0456-0.3719-0.12860.240.0220.1451-0.02990.00520.1648-0.00990.74668.2341-19.793822.92
50.3221.7734-0.05322.0015-0.2330.82180.0464-0.15250.58310.97830.21120.4055-0.20790.0455-0.24710.34030.02760.05130.1889-0.07380.478556.5486-27.92837.0999
61.5041-0.39910.00141.4891-0.20890.64820.11850.28250.0369-0.2561-0.1907-0.27880.18990.05860.09140.20040.02830.06830.1698-0.00710.135549.8586-39.561111.6367
72.66961.2932.10317.05257.46758.1380.0078-0.07380.3523-0.0177-0.54850.4121-0.044-0.56870.52520.18190.00360.04930.14920.00020.229950.8162-36.886722.4578
82.1439-1.54260.34232.58860.03521.76880.22330.3874-0.1881-0.11410.0963-0.27390.39350.2599-0.31380.1804-0.00090.1030.13110.02750.113549.6598-41.224816.5134
94.9362-2.13673.47211.8071-2.39586.60770.0545-0.2601-0.3910.06470.090.15160.1534-0.2829-0.15380.1851-0.01820.05510.0385-0.03580.13847.6849-44.561819.9925
100.74420.5420.20640.4636-0.11951.19060.01740.01390.64050.0262-0.0514-0.32430.0239-0.03520.02910.14250.02340.03360.1649-0.00040.431253.1581-27.304717.2279
114.8181-1.8053-0.15831.4528-0.59921.24240.20120.67230.4091-0.4142-0.2818-0.43890.09140.11550.04560.25030.05840.10350.24070.08620.245152.8151-32.02544.3246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 449 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 58 )
4X-RAY DIFFRACTION4chain 'B' and (resid 59 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 181 through 206 )
6X-RAY DIFFRACTION6chain 'B' and (resid 207 through 282 )
7X-RAY DIFFRACTION7chain 'B' and (resid 283 through 303 )
8X-RAY DIFFRACTION8chain 'B' and (resid 304 through 323 )
9X-RAY DIFFRACTION9chain 'B' and (resid 324 through 353 )
10X-RAY DIFFRACTION10chain 'B' and (resid 354 through 378 )
11X-RAY DIFFRACTION11chain 'B' and (resid 379 through 447 )

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