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- PDB-8aqr: Native crystal structure of the N-terminal beta-hairpin docking (... -

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Basic information

Entry
Database: PDB / ID: 8aqr
TitleNative 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 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

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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)40,4327
Polymers40,3976
Non-polymers351
Water7,350408
1
A: AerJ


Theoretical massNumber of molelcules
Total (without water)6,7331
Polymers6,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AerJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7682
Polymers6,7331
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AerJ


Theoretical massNumber of molelcules
Total (without water)6,7331
Polymers6,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AerJ


Theoretical massNumber of molelcules
Total (without water)6,7331
Polymers6,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: AerJ


Theoretical massNumber of molelcules
Total (without water)6,7331
Polymers6,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: AerJ


Theoretical massNumber of molelcules
Total (without water)6,7331
Polymers6,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.532, 57.391, 62.168
Angle α, β, γ (deg.)90.000, 99.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AerJ / FAD-binding protein


Mass: 6732.778 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.: 408 / 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: 2.11 Å3/Da / Density % sol: 41.78 % / 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: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.46→61.28 Å / Num. obs: 58560 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 10.9 / Num. measured all: 394159
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
1.46-1.496.16.6551851930170.0772.9147.280.3100
7.86-61.2870.016284540910.0060.01777.899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.64 Å61.28 Å
Translation5.79 Å61.28 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.18rc2-3799refinement
PHASER2.8.3phasing
Aimless0.7.4data scaling
XDSMar 15, 2019data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AerJ bHD domain, SeMet derivative

Resolution: 1.46→61.28 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 2834 4.99 %RANDOM
Rwork0.1962 53932 --
obs0.1981 56766 96.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.01 Å2 / Biso mean: 29.5813 Å2 / Biso min: 15.69 Å2
Refinement stepCycle: final / Resolution: 1.46→61.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 1 412 3239
Biso mean--59.68 37.8 -
Num. residues----348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.490.4039830.40571789187264
1.49-1.510.41141270.38842288241583
1.51-1.540.40971310.37492581271295
1.54-1.570.38211290.34992768289799
1.57-1.610.37411590.345827552914100
1.61-1.640.38241530.333927392892100
1.64-1.690.40131460.334227972943100
1.69-1.730.29811520.291627572909100
1.73-1.780.31441510.267827412892100
1.78-1.840.27651680.245927582926100
1.84-1.910.29571580.214927512909100
1.91-1.980.23481270.206228062933100
1.98-2.070.24491470.202527682915100
2.07-2.180.24821350.177627822917100
2.18-2.320.22691490.180427832932100
2.32-2.50.23321390.18628092948100
2.5-2.750.20471410.186327842925100
2.75-3.150.23441280.184328052933100
3.15-3.960.20251480.14928152963100
3.96-61.280.17851630.166828563019100

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