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- PDB-8aqq: SeMet-derived crystal structure of the N-terminal beta-hairpin do... -

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Basic information

Entry
Database: PDB / ID: 8aqq
TitleSeMet-derived crystal structure of the N-terminal beta-hairpin docking (bHD) domain of the AerJ halogenase, from the aeruginosin biosynthetic assembly line
ComponentsAerJ
KeywordsPROTEIN BINDING / beta-hairpin docking domain / nonribosomal peptide synthetase / polyketide synthase / halogenase
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesMicrocystis aeruginosa NIES-98 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsFage, C.D. / Lewandowski, J.R. / Challis, G.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Tandem halogenation and condensation in aeruginosin biosynthesis is directed by docking domain-mediated carrier protein recruitment
Authors: Beech, M.J. / Fage, C.D. / Smith, H.G. / Kosol, S. / Gallo, A. / Bahia, D. / Jenner, M. / Lewandowski, J.R. / Challis, G.L.
History
DepositionAug 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AerJ
B: AerJ
C: AerJ
D: AerJ
E: AerJ
F: AerJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2767
Polymers41,2416
Non-polymers351
Water6,053336
1
A: AerJ


Theoretical massNumber of molelcules
Total (without water)6,8731
Polymers6,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AerJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9092
Polymers6,8731
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AerJ


Theoretical massNumber of molelcules
Total (without water)6,8731
Polymers6,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AerJ


Theoretical massNumber of molelcules
Total (without water)6,8731
Polymers6,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: AerJ


Theoretical massNumber of molelcules
Total (without water)6,8731
Polymers6,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: AerJ


Theoretical massNumber of molelcules
Total (without water)6,8731
Polymers6,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.032, 57.722, 61.907
Angle α, β, γ (deg.)90.000, 99.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AerJ / FAD-binding protein


Mass: 6873.462 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Residues 1-56 of the AerJ halogenase, with an N-terminal Gly-Ser thrombin cleavage scar
Source: (gene. exp.) Microcystis aeruginosa NIES-98 (bacteria)
Gene: aerJ, BFG60_0936 / Plasmid: pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9VVV3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.09 Å3/Da / Density % sol: 41.28 % / Description: Rectangular prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M BICINE (pH 9.0), 2.4 M ammonium sulfate, final pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.68→61.05 Å / Num. obs: 39007 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.056 / Rrim(I) all: 0.211 / Net I/σ(I): 11.7 / Num. measured all: 539586 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.7114.34.6712843019820.2381.2744.8440.899.9
9.05-61.0512.50.05734662780.9990.0160.0653.799.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.18-3840refinement
PHENIX1.14-3260phasing
Aimless0.7.4data scaling
XDSMar 15, 2019data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.68→48.35 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1925 4.94 %RANDOM
Rwork0.188 37038 --
obs0.19 38963 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.91 Å2 / Biso mean: 26.9671 Å2 / Biso min: 10.6 Å2
Refinement stepCycle: final / Resolution: 1.68→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 1 336 3163
Biso mean--55.09 34.42 -
Num. residues----348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.720.37321380.34692631276999
1.72-1.770.38281420.309326272769100
1.77-1.820.29611530.276325942747100
1.82-1.880.27871320.255826302762100
1.88-1.950.28281380.236726312769100
1.95-2.020.25831310.222426472778100
2.02-2.120.25221460.201426262772100
2.12-2.230.24261200.192326762796100
2.23-2.370.2541300.192326362766100
2.37-2.550.25091300.185826312761100
2.55-2.810.22381510.182726562807100
2.81-3.210.20091420.175926432785100
3.21-4.050.18181380.142326852823100
4.05-48.350.19641340.167927252859100

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