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- PDB-7x0f: Structure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant -

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Basic information

Entry
Database: PDB / ID: 7x0f
TitleStructure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant
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
4'-PHOSPHOPANTETHEINE / AMB antimetabolite synthase AmbB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.0Jun 15, 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)225,3168
Polymers223,8834
Non-polymers1,4334
Water12,052669
1
A: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3292
Polymers55,9711
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3292
Polymers55,9711
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3292
Polymers55,9711
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AMB antimetabolite synthase AmbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3292
Polymers55,9711
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.411, 71.190, 172.770
Angle α, β, γ (deg.)90.000, 109.930, 90.000
Int Tables number5
Space group name H-MC121

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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-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
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: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.2→49.56 Å / Num. obs: 114170 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5650 / CC1/2: 0.507 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0261refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X0E

7x0e


Resolution: 2.2→49.56 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 5650 -RANDOM
Rwork0.21 ---
obs-108455 99 %-
Displacement parametersBiso max: 163.46 Å2 / Biso mean: 40.8412 Å2 / Biso min: 13.57 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13813 0 84 669 14566
LS refinement shellResolution: 2.2→2.26 Å
RfactorNum. reflection% reflection
Rfree0.31 --
Rwork0.28 5650 -
obs-7969 99 %

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