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- PDB-7xsi: SdnG, a Diels Alderase catalyzed the formation of norbornene skel... -

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Basic information

Entry
Database: PDB / ID: 7xsi
TitleSdnG, a Diels Alderase catalyzed the formation of norbornene skeleton in Sordarin biosynthetic pathway
ComponentsSordarin/hypoxysordarin biosynthesis cluster protein G
KeywordsBIOSYNTHETIC PROTEIN / pericyclase / Diel Alderase
Function / homologySnoaL-like domain / SnoaL-like domain / antibiotic biosynthetic process / NTF2-like domain superfamily / Sordarin/hypoxysordarin biosynthesis cluster protein G
Function and homology information
Biological speciesSordaria araneosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, B. / Ge, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81991524, 81991522 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Biosynthesis of Sordarin Revealing a Diels-Alderase for the Formation of the Norbornene Skeleton.
Authors: Liu, S.H. / Sun, J.L. / Hu, Y.L. / Zhang, L. / Zhang, X. / Yan, Z.Y. / Guo, X. / Guo, Z.K. / Jiao, R.H. / Zhang, B. / Tan, R.X. / Ge, H.M.
History
DepositionMay 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
SupersessionOct 18, 2023ID: 7XFK
Revision 1.1Oct 18, 2023Group: Advisory / Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_database_PDB_obs_spr / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Sordarin/hypoxysordarin biosynthesis cluster protein G
A: Sordarin/hypoxysordarin biosynthesis cluster protein G
C: Sordarin/hypoxysordarin biosynthesis cluster protein G
D: Sordarin/hypoxysordarin biosynthesis cluster protein G
E: Sordarin/hypoxysordarin biosynthesis cluster protein G
F: Sordarin/hypoxysordarin biosynthesis cluster protein G
G: Sordarin/hypoxysordarin biosynthesis cluster protein G
H: Sordarin/hypoxysordarin biosynthesis cluster protein G


Theoretical massNumber of molelcules
Total (without water)145,2278
Polymers145,2278
Non-polymers00
Water30617
1
B: Sordarin/hypoxysordarin biosynthesis cluster protein G
A: Sordarin/hypoxysordarin biosynthesis cluster protein G


Theoretical massNumber of molelcules
Total (without water)36,3072
Polymers36,3072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-11 kcal/mol
Surface area12850 Å2
MethodPISA
2
C: Sordarin/hypoxysordarin biosynthesis cluster protein G
D: Sordarin/hypoxysordarin biosynthesis cluster protein G


Theoretical massNumber of molelcules
Total (without water)36,3072
Polymers36,3072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-11 kcal/mol
Surface area12960 Å2
MethodPISA
3
E: Sordarin/hypoxysordarin biosynthesis cluster protein G
F: Sordarin/hypoxysordarin biosynthesis cluster protein G


Theoretical massNumber of molelcules
Total (without water)36,3072
Polymers36,3072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-12 kcal/mol
Surface area12730 Å2
MethodPISA
4
G: Sordarin/hypoxysordarin biosynthesis cluster protein G
H: Sordarin/hypoxysordarin biosynthesis cluster protein G


Theoretical massNumber of molelcules
Total (without water)36,3072
Polymers36,3072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-12 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.870, 64.920, 83.990
Angle α, β, γ (deg.)70.580, 72.430, 88.010
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14B
24E
15B
25F
16B
26G
17B
27H
18A
28C
19A
29D
110A
210E
111A
211F
112A
212G
113A
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNALAALABA7 - 13424 - 151
21GLNGLNALAALAAB7 - 13424 - 151
12ILEILELEULEUBA6 - 13523 - 152
22ILEILELEULEUCC6 - 13523 - 152
13GLNGLNALAALABA7 - 13424 - 151
23GLNGLNALAALADD7 - 13424 - 151
14ILEILELEULEUBA6 - 13523 - 152
24ILEILELEULEUEE6 - 13523 - 152
15GLNGLNALAALABA7 - 13424 - 151
25GLNGLNALAALAFF7 - 13424 - 151
16ILEILELEULEUBA6 - 13523 - 152
26ILEILELEULEUGG6 - 13523 - 152
17GLNGLNALAALABA7 - 13424 - 151
27GLNGLNALAALAHH7 - 13424 - 151
18GLNGLNALAALAAB7 - 13424 - 151
28GLNGLNALAALACC7 - 13424 - 151
19GLNGLNHISHISAB7 - 13624 - 153
29GLNGLNHISHISDD7 - 13624 - 153
110GLNGLNALAALAAB7 - 13424 - 151
210GLNGLNALAALAEE7 - 13424 - 151
111GLNGLNHISHISAB7 - 13624 - 153
211GLNGLNHISHISFF7 - 13624 - 153
112GLNGLNALAALAAB7 - 13424 - 151
212GLNGLNALAALAGG7 - 13424 - 151
113GLNGLNHISHISAB7 - 13624 - 153
213GLNGLNHISHISHH7 - 13624 - 153
114GLNGLNALAALACC7 - 13424 - 151
214GLNGLNALAALADD7 - 13424 - 151
115ILEILELEULEUCC6 - 13523 - 152
215ILEILELEULEUEE6 - 13523 - 152
116GLNGLNALAALACC7 - 13424 - 151
216GLNGLNALAALAFF7 - 13424 - 151
117ILEILELEULEUCC6 - 13523 - 152
217ILEILELEULEUGG6 - 13523 - 152
118GLNGLNALAALACC7 - 13424 - 151
218GLNGLNALAALAHH7 - 13424 - 151
119GLNGLNALAALADD7 - 13424 - 151
219GLNGLNALAALAEE7 - 13424 - 151
120GLNGLNHISHISDD7 - 13624 - 153
220GLNGLNHISHISFF7 - 13624 - 153
121GLNGLNALAALADD7 - 13424 - 151
221GLNGLNALAALAGG7 - 13424 - 151
122GLNGLNHISHISDD7 - 13624 - 153
222GLNGLNHISHISHH7 - 13624 - 153
123GLNGLNALAALAEE7 - 13424 - 151
223GLNGLNALAALAFF7 - 13424 - 151
124ILEILELEULEUEE6 - 13523 - 152
224ILEILELEULEUGG6 - 13523 - 152
125GLNGLNALAALAEE7 - 13424 - 151
225GLNGLNALAALAHH7 - 13424 - 151
126GLNGLNALAALAFF7 - 13424 - 151
226GLNGLNALAALAGG7 - 13424 - 151
127GLNGLNHISHISFF7 - 13624 - 153
227GLNGLNHISHISHH7 - 13624 - 153
128GLNGLNALAALAGG7 - 13424 - 151
228GLNGLNALAALAHH7 - 13424 - 151

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Sordarin/hypoxysordarin biosynthesis cluster protein G


Mass: 18153.420 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sordaria araneosa (fungus) / Gene: sdnG
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1B4XBH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium di-hydrogen phosphate, 0.1 M Tris pH 8.5 and 50 % v/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.7→57.99 Å / Num. obs: 28569 / % possible obs: 98.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.087 / Net I/σ(I): 10.1 / Num. measured all: 97465 / Scaling rejects: 54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.833.61.0161343237830.5380.6321.21.497.8
8.95-57.993.80.04230307930.9970.0240.04830.298.4

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→57.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 23.64 / SU ML: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 1831 6.9 %RANDOM
Rwork0.2282 ---
obs0.2317 24674 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 197.47 Å2 / Biso mean: 82.518 Å2 / Biso min: 33.13 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20.43 Å20.33 Å2
2---1.36 Å20.11 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 2.7→57.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8116 0 0 17 8133
Biso mean---48.54 -
Num. residues----1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138260
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157745
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.65211149
X-RAY DIFFRACTIONr_angle_other_deg1.1691.58717912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34851032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.23422.847425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.943151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4491548
X-RAY DIFFRACTIONr_chiral_restr0.0610.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021826
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B37040.11
12A37040.11
21B36950.12
22C36950.12
31B37210.11
32D37210.11
41B37460.11
42E37460.11
51B35980.13
52F35980.13
61B36700.13
62G36700.13
71B36280.13
72H36280.13
81A36290.12
82C36290.12
91A38050.1
92D38050.1
101A36850.11
102E36850.11
111A37080.12
112F37080.12
121A36260.12
122G36260.12
131A36810.12
132H36810.12
141C36690.12
142D36690.12
151C36530.13
152E36530.13
161C35740.13
162F35740.13
171C36520.13
172G36520.13
181C36040.13
182H36040.13
191D36580.11
192E36580.11
201D37250.11
202F37250.11
211D36410.12
212G36410.12
221D37180.12
222H37180.12
231E35840.13
232F35840.13
241E36910.12
242G36910.12
251E35880.13
252H35880.13
261F35600.13
262G35600.13
271F36940.12
272H36940.12
281G36120.13
282H36120.13
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 101 -
Rwork0.431 1476 -
all-1577 -
obs--74.46 %

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