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- PDB-4dg9: Structure of holo-PA1221, an NRPS protein containing adenylation ... -

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Basic information

Entry
Database: PDB / ID: 4dg9
TitleStructure of holo-PA1221, an NRPS protein containing adenylation and PCP domains bound to vinylsulfonamide inhibitor
ComponentsPA1221
KeywordsLIGASE/Inhibitor / ANL Superfamily / Adenylation domain / peptidyl carrier protein / Non-ribosomal peptide synthetase / NRPS / pantetheine / vinylsulfonamide / valine adenylation / LIGASE-Inhibitor complex
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / cytoplasm
Similarity search - Function
ACP-like / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme ...ACP-like / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DG9 / Carrier domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMitchell, C.A. / Shi, C. / Aldrich, C.C. / Gulick, A.M.
CitationJournal: Biochemistry / Year: 2012
Title: Structure of PA1221, a Nonribosomal Peptide Synthetase Containing Adenylation and Peptidyl Carrier Protein Domains.
Authors: Mitchell, C.A. / Shi, C. / Aldrich, C.C. / Gulick, A.M.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 2.0Jun 29, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PA1221
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6432
Polymers67,8571
Non-polymers7861
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.190, 231.180, 122.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PA1221


Mass: 67857.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA1221 / Plasmid: pET15bTEVp21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9I4B7, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Chemical ChemComp-DG9 / 5'-({[(2R,3R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-{[oxido(oxo)phosphonio]oxy}butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-4-methylpentyl]sulfonyl}amino)-5'-deoxyadenosine


Mass: 785.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H48N9O12PS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% Methylether PEG 8000, 50 mM HEPES, 0.18 mM Val-AVS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2010 / Details: SSRL 9-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→55 Å / Num. all: 25006 / Num. obs: 25006 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.4
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DG8

4dg8


Resolution: 2.55→53.97 Å / SU ML: 0.84 / σ(F): 1.35 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 1275 5.1 %
Rwork0.182 --
obs0.185 24977 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.68 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0737 Å20 Å2-0 Å2
2--4.3379 Å20 Å2
3----2.2642 Å2
Refinement stepCycle: LAST / Resolution: 2.55→53.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 0 50 117 4481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084455
X-RAY DIFFRACTIONf_angle_d1.3566069
X-RAY DIFFRACTIONf_dihedral_angle_d16.0711608
X-RAY DIFFRACTIONf_chiral_restr0.095690
X-RAY DIFFRACTIONf_plane_restr0.007798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.65630.35871380.28452604X-RAY DIFFRACTION100
2.6563-2.77720.2841220.25412599X-RAY DIFFRACTION100
2.7772-2.92360.30991410.22862586X-RAY DIFFRACTION100
2.9236-3.10670.2671380.20482620X-RAY DIFFRACTION100
3.1067-3.34660.26051340.18982620X-RAY DIFFRACTION100
3.3466-3.68330.21181490.17422601X-RAY DIFFRACTION100
3.6833-4.21610.20231410.15062634X-RAY DIFFRACTION100
4.2161-5.31110.19281640.13322669X-RAY DIFFRACTION100
5.3111-53.97790.23861480.17972769X-RAY DIFFRACTION99
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)
10.1322-0.01410.02720.0985-0.03080.2176-0.0153-0.0045-0.0496-0.0449-0.022-0.0160.08850.0222-0.03690.06860.01210.00680.0310.01840.03352.1093-53.5518-13.1693
20.12490.1023-0.02190.16110.06070.19550.08480.0477-0.0034-0.1092-0.0277-0.25970.10510.10760.01920.18890.00630.03540.19380.05370.159612.3116-46.6795-19.4583
30.4205-0.0501-0.1270.2722-0.0470.2342-0.0351-0.1080.07630.05490.05180.0363-0.01230.00190.00980.02420.02560.02860.0743-0.0140.0649-8.2286-39.1915-2.672
40.16510.09580.02550.4567-0.05660.06080.0342-0.1980.00270.323-0.067-0.0438-0.0210.0696-0.01130.27370.013-0.04010.3206-0.03390.09454.6609-37.570113.2333
50.42090.0938-0.31380.2587-0.01490.3878-0.0429-0.08850.1723-0.05240.04780.0356-0.16780.06-0.05230.2569-0.0106-0.03160.0767-0.0440.29490.7158-15.7269-8.3642
60.1177-0.11550.06970.34170.26340.5237-0.02050.24910.1702-0.18350.1060.13930.0915-0.04320.39530.2301-0.0208-0.06480.29590.16480.2868-11.6244-18.2808-25.9025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 16:110)
2X-RAY DIFFRACTION2chain 'A' and (resseq 111:158)
3X-RAY DIFFRACTION3chain 'A' and (resseq 159:375)
4X-RAY DIFFRACTION4chain 'A' and (resseq 376:404)
5X-RAY DIFFRACTION5chain 'A' and (resseq 405:535)
6X-RAY DIFFRACTION6chain 'A' and (resseq 536:602)

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