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- PDB-7x0e: Structure of Pseudomonas NRPS protein, AmbB-TC in apo form -

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Basic information

Entry
Database: PDB / ID: 7x0e
TitleStructure of Pseudomonas NRPS protein, AmbB-TC in apo form
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 / cytosol / 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 / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / 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 / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / 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-7Z8 / AMB antimetabolite synthase AmbB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3062
Polymers55,9711
Non-polymers3351
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.910, 87.910, 285.421
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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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.: 1
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-7Z8 / N-methyl-N-[(2S,3R,4R,5R)-2,3,4,5,6-pentakis(oxidanyl)hexyl]nonanamide / MEGA-9


Mass: 335.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H33NO6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Tris pH 7.5, 11% PEG 6000, 2.5% EG/MPD, 25mM MEGA-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→52.06 Å / Num. obs: 38654 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.13 Å2 / CC1/2: 0.98 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.21 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5494 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→39.9 Å / SU ML: 0.3193 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0085
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 1917 4.96 %RANDOM
Rwork0.2276 36737 --
obs0.2297 38654 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.62 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 23 159 3112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023051
X-RAY DIFFRACTIONf_angle_d0.48144150
X-RAY DIFFRACTIONf_chiral_restr0.0368487
X-RAY DIFFRACTIONf_plane_restr0.0033539
X-RAY DIFFRACTIONf_dihedral_angle_d4.2507446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.36881320.31942546X-RAY DIFFRACTION98.46
2.15-2.210.40081150.31152579X-RAY DIFFRACTION98.54
2.21-2.280.35921400.2962551X-RAY DIFFRACTION98.64
2.28-2.350.32581480.29022557X-RAY DIFFRACTION98.69
2.35-2.430.36411260.29672593X-RAY DIFFRACTION98.84
2.43-2.530.33461370.28322585X-RAY DIFFRACTION98.95
2.53-2.650.33821640.26752565X-RAY DIFFRACTION98.95
2.65-2.790.29881310.26632608X-RAY DIFFRACTION99.28
2.79-2.960.30331440.25962623X-RAY DIFFRACTION99.32
2.96-3.190.25471320.2412654X-RAY DIFFRACTION99.36
3.19-3.510.25211570.22132640X-RAY DIFFRACTION99.33
3.51-4.020.22391200.20422725X-RAY DIFFRACTION99.72
4.02-5.060.24241290.17322734X-RAY DIFFRACTION99.38
5.06-39.90.23021420.19952777X-RAY DIFFRACTION93.98

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