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- PDB-6a5g: The structure of [4+2] and [6+4] cyclase in the biosynthetic path... -

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Basic information

Entry
Database: PDB / ID: 6a5g
TitleThe structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of streptoseomycin
Components[4+2] and [4+6] cyclase StmD
KeywordsBIOSYNTHETIC PROTEIN / [4+2] and [4+6] cyclase / Streptoseomycin / biosynthesis
Biological speciesStreptomyces seoulensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, B. / Ge, H.M.
Funding support China, 8items
OrganizationGrant numberCountry
National Natural Science Foundation of China21572100 China
National Natural Science Foundation of China81522042 China
National Natural Science Foundation of China81773591 China
National Natural Science Foundation of China81421091 China
National Natural Science Foundation of China81500059 China
National Natural Science Foundation of China81673333 China
National Natural Science Foundation of China21672101 China
National Natural Science Foundation of China21661140001 China
CitationJournal: Nature / Year: 2019
Title: Enzyme-catalysed [6+4] cycloadditions in the biosynthesis of natural products.
Authors: Zhang, B. / Wang, K.B. / Wang, W. / Wang, X. / Liu, F. / Zhu, J. / Shi, J. / Li, L.Y. / Han, H. / Xu, K. / Qiao, H.Y. / Zhang, X. / Jiao, R.H. / Houk, K.N. / Liang, Y. / Tan, R.X. / Ge, H.M.
History
DepositionJun 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: [4+2] and [4+6] cyclase StmD
C: [4+2] and [4+6] cyclase StmD
D: [4+2] and [4+6] cyclase StmD
B: [4+2] and [4+6] cyclase StmD


Theoretical massNumber of molelcules
Total (without water)72,6484
Polymers72,6484
Non-polymers00
Water4,522251
1
A: [4+2] and [4+6] cyclase StmD
D: [4+2] and [4+6] cyclase StmD


Theoretical massNumber of molelcules
Total (without water)36,3242
Polymers36,3242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-16 kcal/mol
Surface area13940 Å2
MethodPISA
2
C: [4+2] and [4+6] cyclase StmD
B: [4+2] and [4+6] cyclase StmD


Theoretical massNumber of molelcules
Total (without water)36,3242
Polymers36,3242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-16 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.109, 85.023, 134.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 3 through 117 or (resid 118...
31(chain C and (resid 3 through 117 or (resid 118...
41(chain D and (resid 3 through 117 or (resid 118...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRchain AAA3 - 1523 - 152
21TRPTRP(chain B and (resid 3 through 117 or (resid 118...BD3 - 1173 - 117
22GLUGLU(chain B and (resid 3 through 117 or (resid 118...BD118118
23GLUGLU(chain B and (resid 3 through 117 or (resid 118...BD3 - 1593 - 159
24GLUGLU(chain B and (resid 3 through 117 or (resid 118...BD3 - 1593 - 159
25GLUGLU(chain B and (resid 3 through 117 or (resid 118...BD3 - 1593 - 159
26GLUGLU(chain B and (resid 3 through 117 or (resid 118...BD3 - 1593 - 159
31TRPTRP(chain C and (resid 3 through 117 or (resid 118...CB3 - 1173 - 117
32GLUGLU(chain C and (resid 3 through 117 or (resid 118...CB118118
33TYRTYR(chain C and (resid 3 through 117 or (resid 118...CB3 - 1523 - 152
41TRPTRP(chain D and (resid 3 through 117 or (resid 118...DC3 - 1173 - 117
42GLUGLU(chain D and (resid 3 through 117 or (resid 118...DC118118
43TYRTYR(chain D and (resid 3 through 117 or (resid 118...DC3 - 1523 - 152

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Components

#1: Protein
[4+2] and [4+6] cyclase StmD


Mass: 18161.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces seoulensis (bacteria) / Strain: A01
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 M ammonium sulfate, 100 mM MES, pH 6.5, 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→48.604 Å / Num. obs: 24828 / % possible obs: 90.65 % / Redundancy: 6.4 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.199 / Net I/σ(I): 20.93
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A5F

6a5f


Resolution: 2.3→48.604 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.91
RfactorNum. reflection% reflection
Rfree0.246 1989 8.01 %
Rwork0.1796 --
obs0.1849 24828 90.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.35 Å2 / Biso mean: 28.26 Å2 / Biso min: 12.26 Å2
Refinement stepCycle: final / Resolution: 2.3→48.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 0 251 4932
Biso mean---29 -
Num. residues----607
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2777X-RAY DIFFRACTION13.688TORSIONAL
12B2777X-RAY DIFFRACTION13.688TORSIONAL
13C2777X-RAY DIFFRACTION13.688TORSIONAL
14D2777X-RAY DIFFRACTION13.688TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2999-2.35740.28621510.20291728187998
2.3574-2.42120.27751510.18461727187899
2.4212-2.49240.28231540.17821776193099
2.4924-2.57290.29281500.18821738188899
2.5729-2.66480.28511100.19111255136597
2.6648-2.77150.29291000.20361132123298
2.7715-2.89760.27461570.199117951952100
2.8976-3.05040.24891540.193317771931100
3.0504-3.24150.25231560.183417791935100
3.2415-3.49170.25171180.18471367148576
3.4917-3.84290.23691250.17761438156380
3.8429-4.39870.20561340.15271548168285
4.3987-5.54060.19981610.152118442005100
5.5406-48.61460.23361680.19011935210399
Refinement TLS params.Method: refined / Origin x: 15.0069 Å / Origin y: 20.5172 Å / Origin z: 37.2269 Å
111213212223313233
T0.159 Å20.0034 Å2-0.0201 Å2-0.1431 Å20.0081 Å2--0.1889 Å2
L0.4791 °20.0085 °2-0.1021 °2-0.4012 °20.2311 °2--1.0118 °2
S-0.0049 Å °-0.0016 Å °0.0655 Å °-0.007 Å °0.0045 Å °-0.0316 Å °-0.1146 Å °0.0466 Å °-0.0015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 152
2X-RAY DIFFRACTION1allC3 - 152
3X-RAY DIFFRACTION1allD3 - 152
4X-RAY DIFFRACTION1allB3 - 159

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