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- PDB-7z6p: Diels-Alderase AbyU mutant - Y76F -

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Basic information

Entry
Database: PDB / ID: 7z6p
TitleDiels-Alderase AbyU mutant - Y76F
ComponentsYD repeat-containing protein
KeywordsBIOSYNTHETIC PROTEIN / The Y76F mutant of WT Diels-Alderase protein AbyU / which catalyses the cyclisation of spirotetronate precursor of abyssomicin C and atrop-abyssomicin C.
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
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / chem_comp_atom / chem_comp_bond / citation_author / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_assembly / refine
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_contact_author.id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: YD repeat-containing protein
BBB: YD repeat-containing protein
CCC: YD repeat-containing protein
DDD: YD repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3598
Polymers62,4064
Non-polymers9534
Water8,719484
1
AAA: YD repeat-containing protein
BBB: YD repeat-containing protein
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 31.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)31,6804
Polymers31,2032
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint1 kcal/mol
Surface area12210 Å2
MethodPISA
2
CCC: YD repeat-containing protein
DDD: YD repeat-containing protein
hetero molecules


  • defined by author&software
  • 31.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)31,6804
Polymers31,2032
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint2 kcal/mol
Surface area11840 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: 15601.507 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora maris AB-18-032 (bacteria)
Strain: DSM 45365 / JCM 31040 / NBRC 109089 / NRRL B-24793 / AB-18-032
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 / HEPES


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


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 293.15 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: 100 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→40.54 Å / Mean I/σ(I) obs: 11.3 / Num. unique obs: 84307 / CC1/2: 1 / Rrim(I) all: 0.047

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dyv

5dyv


Resolution: 1.56→40.577 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.209 4233 5.021 %
Rwork0.176 80073 -
all0.179 --
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: 37.759 Å2
Baniso -1Baniso -2Baniso -3
1-2.611 Å2-0.81 Å20.142 Å2
2---2.349 Å2-0.484 Å2
3----0.109 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_d0.0120.0134322
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174020
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6645878
X-RAY DIFFRACTIONr_angle_other_deg2.4241.6119283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.935540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.21521.897232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76715672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6411532
X-RAY DIFFRACTIONr_chiral_restr0.0850.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024850
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02958
X-RAY DIFFRACTIONr_nbd_refined0.20.2647
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.23703
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22042
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.120.22023
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2416
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1070.23
X-RAY DIFFRACTIONr_nbd_other0.1250.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.218
X-RAY DIFFRACTIONr_mcbond_it3.3933.62136
X-RAY DIFFRACTIONr_mcbond_other3.3863.5992135
X-RAY DIFFRACTIONr_mcangle_it4.9565.3752666
X-RAY DIFFRACTIONr_mcangle_other4.9575.3752667
X-RAY DIFFRACTIONr_scbond_it4.3594.1522186
X-RAY DIFFRACTIONr_scbond_other4.3574.1522186
X-RAY DIFFRACTIONr_scangle_it6.5866.0253206
X-RAY DIFFRACTIONr_scangle_other6.5856.0263207
X-RAY DIFFRACTIONr_lrange_it9.14243.7724775
X-RAY DIFFRACTIONr_lrange_other9.10142.9024620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.323050.3265842X-RAY DIFFRACTION94.6275
1.6-1.6440.3432960.3055728X-RAY DIFFRACTION94.5089
1.644-1.6920.3153080.2915607X-RAY DIFFRACTION95.2649
1.692-1.7440.2592990.2555386X-RAY DIFFRACTION94.829
1.744-1.8010.2612910.2435317X-RAY DIFFRACTION95.8633
1.801-1.8640.2482530.2135112X-RAY DIFFRACTION95.7523
1.864-1.9350.2272460.2034980X-RAY DIFFRACTION96.1899
1.935-2.0130.2282480.1874836X-RAY DIFFRACTION96.3061
2.013-2.1030.2232510.1964572X-RAY DIFFRACTION96.6727
2.103-2.2050.2212340.1874413X-RAY DIFFRACTION97.1566
2.205-2.3250.2072060.1734233X-RAY DIFFRACTION96.9426
2.325-2.4650.222170.1623990X-RAY DIFFRACTION97.1818
2.465-2.6350.1932000.1663717X-RAY DIFFRACTION97.0515
2.635-2.8460.2152180.1713451X-RAY DIFFRACTION96.6289
2.846-3.1170.2211780.183136X-RAY DIFFRACTION95.808
3.117-3.4840.1951260.1752804X-RAY DIFFRACTION93.4311
3.484-4.020.1961160.1592494X-RAY DIFFRACTION93.9863
4.02-4.9180.1271310.1282060X-RAY DIFFRACTION93.1944
4.918-6.9320.212640.1681600X-RAY DIFFRACTION92.1373
6.932-40.5770.19460.199796X-RAY DIFFRACTION84.0319

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