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- PDB-5dyq: AbyU L73M L139M -

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Basic information

Entry
Database: PDB / ID: 5dyq
TitleAbyU L73M L139M
ComponentsYD repeat-containing protein
KeywordsLIGASE / [4+2] cycloaddition / Diels-Alderase / Diels-Alder / 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 / SAD / Resolution: 1.66 Å
AuthorsByrne, M.J. / Race, P.R.
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

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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)72,8537
Polymers72,1384
Non-polymers7153
Water1,74797
1
D: YD repeat-containing protein
hetero molecules

A: YD repeat-containing protein


Theoretical massNumber of molelcules
Total (without water)36,3073
Polymers36,0692
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area2180 Å2
ΔGint-6 kcal/mol
Surface area11390 Å2
MethodPISA
2
B: YD repeat-containing protein
C: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5464
Polymers36,0692
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-1 kcal/mol
Surface area11140 Å2
MethodPISA
3
A: YD repeat-containing protein

D: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3073
Polymers36,0692
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area2180 Å2
ΔGint-6 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.351, 68.270, 139.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A10 - 140
2010B10 - 140
1020A10 - 139
2020C10 - 139
1030A10 - 140
2030D10 - 140
1040B10 - 139
2040C10 - 139
1050B10 - 140
2050D10 - 140
1060C10 - 139
2060D10 - 139

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
YD repeat-containing protein / AbyU


Mass: 18034.451 Da / Num. of mol.: 4 / Mutation: L73M, L139M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucosispora maris (bacteria) / Gene: VAB18032_16470, AbyU / Plasmid: pOPINF / 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 / HEPES


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


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.79 Å3/Da / Density % sol: 55.85 % / Description: Rhomboid
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M magnesium chloride, 0.1 M HEPES 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: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.66→68.27 Å / Num. obs: 65871 / % possible obs: 86.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALAdata scaling
MOSFLMdata reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→61.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.547 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21136 3375 5.1 %RANDOM
Rwork0.18956 ---
obs0.19068 62463 85.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.466 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.66→61.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 45 97 4192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.024192
X-RAY DIFFRACTIONr_bond_other_d0.0110.023937
X-RAY DIFFRACTIONr_angle_refined_deg2.1841.9655693
X-RAY DIFFRACTIONr_angle_other_deg1.72239022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50823.474190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50515617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2691532
X-RAY DIFFRACTIONr_chiral_restr0.1170.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024783
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02973
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73770.09
12B73770.09
21A72950.1
22C72950.1
31A73850.09
32D73850.09
41B73520.11
42C73520.11
51B73240.1
52D73240.1
61C75370.09
62D75370.09
LS refinement shellResolution: 1.657→1.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 202 -
Rwork0.231 4328 -
obs--80.82 %

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