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- PDB-6ymn: Crystal structure of the Diels Alderase AbmU from Streptomyces ko... -

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Basic information

Entry
Database: PDB / ID: 6ymn
TitleCrystal structure of the Diels Alderase AbmU from Streptomyces koyangensis
ComponentsAbmU
KeywordsLIGASE / Enzyme / Diels Alderase / neoabyssomicin / abyssomicin / Streptomyces koyangensis
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / antibiotic biosynthetic process / isomerase activity / BROMIDE ION / AbmU
Function and homology information
Biological speciesStreptomyces koyangensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsBack, C.R. / Burton, N. / Race, P.R.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T001968/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M012107/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G0367641/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the Diels Alderase AbmU from Streptomyces koyangensis
Authors: Back, C.R. / Mbatha, S. / Johns, S. / Burton, N. / Tiwari, K. / van der Kamp, M. / Willis, C. / Race, P.R.
History
DepositionApr 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: AbmU
BBB: AbmU
CCC: AbmU
DDD: AbmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,25411
Polymers102,6944
Non-polymers5597
Water8,737485
1
AAA: AbmU
BBB: AbmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6676
Polymers51,3472
Non-polymers3204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-38 kcal/mol
Surface area17140 Å2
MethodPISA
2
CCC: AbmU
DDD: AbmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5875
Polymers51,3472
Non-polymers2403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-34 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.128, 64.998, 97.865
Angle α, β, γ (deg.)90.000, 93.813, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AbmU


Mass: 25673.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces koyangensis (bacteria) / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2P1BT29
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M Na acetate, 0.1 M Na cacodylate, 32% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9197 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.05→56.44 Å / Num. obs: 52059 / % possible obs: 99.8 % / Redundancy: 18.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.043 / Net I/σ(I): 12.25
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 1.502 / Num. unique obs: 2522 / Rpim(I) all: 0.681 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
DIALSdata reduction
xia2data scaling
CRANK22.0.229phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→56.44 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.171 / Average fsc free: 0.8868 / Average fsc work: 0.8978 / Cross valid method: FREE R-VALUE / ESU R: 0.216 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2427 2616 5.027 %
Rwork0.1889 49419 -
all0.192 --
obs-52035 99.585 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.298 Å20 Å2-0.627 Å2
2--0.846 Å20 Å2
3---1.522 Å2
Refinement stepCycle: LAST / Resolution: 2.05→56.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6228 0 7 485 6720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136446
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175779
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.6488809
X-RAY DIFFRACTIONr_angle_other_deg2.3611.56713372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4385811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.55320.737353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3771555
X-RAY DIFFRACTIONr_chiral_restr0.0750.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027391
X-RAY DIFFRACTIONr_gen_planes_other0.010.021446
X-RAY DIFFRACTIONr_nbd_refined0.210.21295
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.25646
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23013
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2467
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.5930.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.218
X-RAY DIFFRACTIONr_nbd_other0.1950.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.214
X-RAY DIFFRACTIONr_mcbond_it2.9964.023247
X-RAY DIFFRACTIONr_mcbond_other2.9964.023246
X-RAY DIFFRACTIONr_mcangle_it4.5536.0044045
X-RAY DIFFRACTIONr_mcangle_other4.5536.0054046
X-RAY DIFFRACTIONr_scbond_it3.2414.3553199
X-RAY DIFFRACTIONr_scbond_other3.2414.3563200
X-RAY DIFFRACTIONr_scangle_it4.9336.4254760
X-RAY DIFFRACTIONr_scangle_other4.9336.4264761
X-RAY DIFFRACTIONr_lrange_it7.71748.1497150
X-RAY DIFFRACTIONr_lrange_other7.62547.8087027
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.05-2.1030.3081870.30235820.30238380.7920.78198.20220.3
2.103-2.160.2991710.27535340.27637350.8070.81299.19680.266
2.16-2.2230.2731570.25934610.25936430.8350.83799.31380.249
2.223-2.2910.3071460.23533700.23835390.8340.85999.35010.219
2.291-2.3660.2741500.21832350.22134030.8830.89399.47110.202
2.366-2.4490.2811640.231720.20433490.8810.90899.61180.179
2.449-2.5410.3051670.21330090.21731840.8740.89999.74870.19
2.541-2.6450.2741530.18929330.19330970.8950.92399.64480.168
2.645-2.7620.2621310.18928120.19229490.8990.92499.79650.166
2.762-2.8970.2931330.20527040.2128420.8790.90799.82410.184
2.897-3.0530.2641590.19825090.20226720.9060.92999.85030.179
3.053-3.2380.2611520.19523970.19925500.9150.93599.96080.179
3.238-3.460.2611350.18422920.18824280.9080.94199.95880.171
3.46-3.7360.1981270.16721060.16922330.9550.9521000.158
3.736-4.0910.1991190.15519500.15720690.9540.9581000.15
4.091-4.5710.2071090.14417630.14818730.9530.9699.94660.142
4.571-5.2730.211020.14315640.14716660.9480.9621000.142
5.273-6.4430.207670.18513480.18614150.9490.9521000.182
6.443-9.0540.223540.17110640.17311180.9420.9591000.172
9.054-56.440.256330.2076140.2096470.9340.951000.214

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