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- PDB-7x17: Structure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant-L-Ala -

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Basic information

Entry
Database: PDB / ID: 7x17
TitleStructure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant-L-Ala
ComponentsAMB antimetabolite synthase AmbB
KeywordsBIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / AmbB / Pseudomonas
Function / homology
Function and homology information


L-alanine-[L-alanyl-carrier protein] ligase / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / ligase activity / cytoplasm
Similarity search - Function
Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily ...Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / 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
Similarity search - Domain/homology
Chem-868 / AMB antimetabolite synthase AmbB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChuYuanKee, M. / Bharath, S.R. / Song, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2022
Title: Structural insights into the substrate-bound condensation domains of non-ribosomal peptide synthetase AmbB.
Authors: Chu Yuan Kee, M.J. / Bharath, S.R. / Wee, S. / Bowler, M.W. / Gunaratne, J. / Pan, S. / Zhang, L. / Song, H.
History
DepositionFeb 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMB antimetabolite synthase AmbB
B: AMB antimetabolite synthase AmbB
C: AMB antimetabolite synthase AmbB
D: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,6008
Polymers223,8834
Non-polymers1,7184
Water7,494416
1
A: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4002
Polymers55,9711
Non-polymers4291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4002
Polymers55,9711
Non-polymers4291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4002
Polymers55,9711
Non-polymers4291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4002
Polymers55,9711
Non-polymers4291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.498, 71.610, 173.757
Angle α, β, γ (deg.)90.000, 110.140, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein
AMB antimetabolite synthase AmbB / L-alanine--[L-alanyl-carrier protein] ligase / Nonribosomal peptide synthase AmbB


Mass: 55970.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: ambB, PA2305 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I1H0, L-alanine-[L-alanyl-carrier protein] ligase
#2: Chemical
ChemComp-868 / S-[2-[3-[[(2S)-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (2R)-2-azanylpropanethioate


Mass: 429.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28N3O8PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M MES pH 6.6, 0.2M ammonium nitrate, 15% PEG 3350, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.83 Å / Num. obs: 78940 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.52 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.55 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4499 / CC1/2: 0.559

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X0E

7x0e


Resolution: 2.5→46.59 Å / SU ML: 0.3807 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.8858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.299 3952 5.01 %RANDOM
Rwork0.2464 74922 --
obs0.249 78874 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13273 0 104 416 13793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001913592
X-RAY DIFFRACTIONf_angle_d0.460318456
X-RAY DIFFRACTIONf_chiral_restr0.03582158
X-RAY DIFFRACTIONf_plane_restr0.00382409
X-RAY DIFFRACTIONf_dihedral_angle_d10.0691959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.37661550.31262640X-RAY DIFFRACTION99.5
2.53-2.560.31541550.30242707X-RAY DIFFRACTION99.48
2.56-2.60.34771480.30212609X-RAY DIFFRACTION99.49
2.6-2.630.34991340.292700X-RAY DIFFRACTION99.47
2.63-2.670.34461220.29652643X-RAY DIFFRACTION99.5
2.67-2.710.33061510.2832711X-RAY DIFFRACTION99.69
2.71-2.750.32581360.2752680X-RAY DIFFRACTION99.65
2.75-2.80.31361350.28232649X-RAY DIFFRACTION99.78
2.8-2.840.37011570.28282716X-RAY DIFFRACTION99.65
2.84-2.90.37391320.27622654X-RAY DIFFRACTION99.75
2.9-2.950.32651470.27432661X-RAY DIFFRACTION99.75
2.95-3.010.30541420.25562730X-RAY DIFFRACTION99.72
3.01-3.080.33911380.25732660X-RAY DIFFRACTION99.89
3.08-3.150.31951420.26952685X-RAY DIFFRACTION99.82
3.15-3.230.32551420.25742701X-RAY DIFFRACTION99.72
3.23-3.320.2961350.262719X-RAY DIFFRACTION99.96
3.32-3.410.30021520.25092714X-RAY DIFFRACTION99.76
3.41-3.520.28961410.24172637X-RAY DIFFRACTION99.5
3.52-3.650.32531460.22782706X-RAY DIFFRACTION99.69
3.65-3.80.2981600.22162656X-RAY DIFFRACTION99.4
3.8-3.970.3111330.2322706X-RAY DIFFRACTION99.06
3.97-4.180.25841210.22052711X-RAY DIFFRACTION99.23
4.18-4.440.2771310.21082699X-RAY DIFFRACTION99.16
4.44-4.780.24481270.20262711X-RAY DIFFRACTION98.89
4.78-5.260.26931300.21042697X-RAY DIFFRACTION98.64
5.26-6.020.28431490.25262694X-RAY DIFFRACTION99.09
6.02-7.580.27451560.24772709X-RAY DIFFRACTION98.42
7.58-46.590.20721350.20522417X-RAY DIFFRACTION85.35

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