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- PDB-8qfu: Diels-Alderase AbyU mutant - Y76F -

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Basic information

Entry
Database: PDB / ID: 8qfu
TitleDiels-Alderase AbyU mutant - Y76F
ComponentsYD repeat-containing protein
KeywordsLIGASE / The Y76F mutant of WT Diels-Alderase protein AbyU / which catalyses the cyclisation of spirotetronate precursor of abyssomicin C and atrop-abyssomicin C. / BIOSYNTHETIC PROTEIN
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / antibiotic biosynthetic process / isomerase activity / YD repeat-containing protein
Function and homology information
Biological speciesMicromonospora maris AB-18-032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsTiwari, K. / Burton, N.M. / Yang, S. / Race, P.R.
Funding support United Kingdom, 3items
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/M025624/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of Diels-Alderase AbyU mutant Y76F at 1.56 Angstroms resolution.
Authors: Tiwari, K. / Burton, N.M. / Yang, S. / Race, P.R.
History
DepositionSep 5, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionSep 18, 2024ID: 7Z6P
Revision 1.0Sep 18, 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: YD repeat-containing protein
B: YD repeat-containing protein
C: YD repeat-containing protein
D: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9458
Polymers70,9924
Non-polymers9534
Water8,719484
1
A: YD repeat-containing protein
B: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9724
Polymers35,4962
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint2 kcal/mol
Surface area12210 Å2
MethodPISA
2
C: YD repeat-containing protein
D: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9724
Polymers35,4962
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint2 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.710, 53.820, 60.480
Angle α, β, γ (deg.)90.110, 96.980, 94.660
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
YD repeat-containing protein


Mass: 17747.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora maris AB-18-032 (bacteria)
Gene: VAB18032_16470 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4F7G1
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.25 M Magnesium Chloride 0.1M HEPES 10% PEG 6K

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→40.58 Å / Num. obs: 84307 / % possible obs: 95.5 % / Redundancy: 3.5 % / Rrim(I) all: 0.033 / Net I/σ(I): 11.3
Reflection shellResolution: 1.56→1.59 Å / Num. unique obs: 84307 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→40.577 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.374 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2079 4233 5.021 %
Rwork0.1724 80073 -
all0.174 --
obs-84306 95.462 %
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: 36.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.576 Å2-0.799 Å20.12 Å2
2---2.337 Å2-0.487 Å2
3----0.083 Å2
Refinement stepCycle: LAST / Resolution: 1.56→40.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 60 484 4664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124307
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164054
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.6545858
X-RAY DIFFRACTIONr_angle_other_deg0.6541.5749318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.147532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77510672
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.15310200
X-RAY DIFFRACTIONr_chiral_restr0.1010.2655
X-RAY DIFFRACTIONr_chiral_restr_other0.0240.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
X-RAY DIFFRACTIONr_nbd_refined0.2060.2677
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23732
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22058
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.22381
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2432
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1070.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.23
X-RAY DIFFRACTIONr_nbd_other0.0980.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.215
X-RAY DIFFRACTIONr_mcbond_it4.3163.5832136
X-RAY DIFFRACTIONr_mcbond_other4.3123.5832136
X-RAY DIFFRACTIONr_mcangle_it5.8596.3922666
X-RAY DIFFRACTIONr_mcangle_other5.866.3922667
X-RAY DIFFRACTIONr_scbond_it5.9014.1912171
X-RAY DIFFRACTIONr_scbond_other5.8614.1872169
X-RAY DIFFRACTIONr_scangle_it8.5427.4223186
X-RAY DIFFRACTIONr_scangle_other8.5417.4243187
X-RAY DIFFRACTIONr_lrange_it10.4837.5584789
X-RAY DIFFRACTIONr_lrange_other10.50435.5374624
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
1.56-1.60.3263050.32858370.32864910.8840.89294.62330.331
1.6-1.6440.3382950.30457240.30563680.8880.9194.51950.302
1.644-1.6920.3193090.2955980.29162020.8960.9295.24350.283
1.692-1.7440.2712980.2553840.25159920.9390.94394.82640.24
1.744-1.8010.2742910.23553140.23758450.9450.95895.89390.223
1.801-1.8640.2562540.20651120.20956050.9560.96995.73590.194
1.864-1.9340.2242450.19149730.19254250.9660.97396.18430.177
1.934-2.0130.2252470.18148340.18352740.9650.97896.34050.173
2.013-2.1020.2272510.18645680.18849850.9660.97896.670.18
2.102-2.2050.2242350.1844170.18347900.9670.97997.1190.178
2.205-2.3230.212050.16542280.16745730.9730.98396.93860.166
2.323-2.4640.2242170.15439930.15743320.9670.98597.18370.16
2.464-2.6330.2012010.15937130.16140340.9750.98497.02530.168
2.633-2.8430.2142150.16534540.16837940.970.98396.70530.18
2.843-3.1130.231780.17731360.18134590.9710.98195.8080.204
3.113-3.4780.2011280.17527990.17631330.9760.98493.42480.201
3.478-4.0110.2031170.15525040.15727850.9740.98794.11130.185
4.011-4.9010.131310.12220650.12223570.9890.99293.16930.157
4.901-6.8810.215630.16416040.16618080.9820.98892.20130.202
6.881-40.5770.197480.28160.210270.9780.97484.12850.261

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