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- PDB-5dyv: AbyU - wildtype -

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Basic information

Entry
Database: PDB / ID: 5dyv
TitleAbyU - wildtype
ComponentsYD repeat-containing protein
KeywordsLIGASE / AbyU / Diels-Alderase / Diels-Alder / Cyclase / [4+2] cycloaddition / tetronate / spirotetronate / polyketide / Abyssomicin
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 speciesVerrucosispora maris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRace, P.R. / Byrne, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L01386X/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail.
Authors: Byrne, M.J. / Lees, N.R. / Han, L.C. / van der Kamp, M.W. / Mulholland, A.J. / Stach, J.E. / Willis, C.L. / Race, P.R.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
A: YD repeat-containing protein
B: YD repeat-containing protein
C: YD repeat-containing protein
D: YD repeat-containing protein
E: YD repeat-containing protein
F: YD repeat-containing protein
G: YD repeat-containing protein
H: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,01816
Polymers142,1118
Non-polymers1,9068
Water91951
1
A: YD repeat-containing protein
H: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0044
Polymers35,5282
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint2 kcal/mol
Surface area11820 Å2
MethodPISA
2
B: YD repeat-containing protein
F: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0044
Polymers35,5282
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint2 kcal/mol
Surface area11660 Å2
MethodPISA
3
C: YD repeat-containing protein
E: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0044
Polymers35,5282
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint3 kcal/mol
Surface area11750 Å2
MethodPISA
4
D: YD repeat-containing protein
G: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0044
Polymers35,5282
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-0 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.800, 73.590, 86.190
Angle α, β, γ (deg.)112.87, 90.04, 89.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
YD repeat-containing protein / AbyU


Mass: 17763.900 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucosispora maris (bacteria) / Gene: VAB18032_16470 / Production host: Escherichia coli B (bacteria) / Strain (production host): b834 / References: UniProt: F4F7G1
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.55 % / Description: Rhomboid
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M magnesium chloride, 0.1 M HEPES pH 7.5 18% w/v poly(acrylic acid) sodium salt MW 5100

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.36→79.41 Å / Num. all: 172193 / Num. obs: 52922 / % possible obs: 92.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.4
Reflection shellHighest resolution: 2.36 Å / Rmerge(I) obs: 0.358

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→79.41 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.863 / SU B: 9.23 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25298 2321 5 %RANDOM
Rwork0.19665 ---
obs0.19946 43757 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.474 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20.59 Å2-0.07 Å2
2---0.7 Å20.15 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→79.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8157 0 120 51 8328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.028449
X-RAY DIFFRACTIONr_bond_other_d0.0020.027993
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.96311485
X-RAY DIFFRACTIONr_angle_other_deg0.997318312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19251047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18723.245379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.324151301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1111568
X-RAY DIFFRACTIONr_chiral_restr0.1210.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021955
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3062.164212
X-RAY DIFFRACTIONr_mcbond_other1.3062.164211
X-RAY DIFFRACTIONr_mcangle_it2.13.2375251
X-RAY DIFFRACTIONr_mcangle_other2.13.2375252
X-RAY DIFFRACTIONr_scbond_it1.5822.2964237
X-RAY DIFFRACTIONr_scbond_other1.5822.2964237
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5413.3756235
X-RAY DIFFRACTIONr_long_range_B_refined3.65816.8558811
X-RAY DIFFRACTIONr_long_range_B_other3.65516.8568809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 177 -
Rwork0.249 3346 -
obs--96.79 %

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