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- PDB-6a5h: The structure of [4+2] and [6+4] cyclase in the biosynthetic path... -

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Basic information

Entry
Database: PDB / ID: 6a5h
TitleThe structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of unidentified natural product
Components101015D
KeywordsBIOSYNTHETIC PROTEIN / [4+2] and [4+6] cyclase / natural product / biosynthesis
Biological speciesNocardia tenerifensis NBRC 101015 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.618 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

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Assembly

Deposited unit
A: 101015D
B: 101015D


Theoretical massNumber of molelcules
Total (without water)36,4402
Polymers36,4402
Non-polymers00
Water7,494416
1
A: 101015D
B: 101015D

A: 101015D
B: 101015D


Theoretical massNumber of molelcules
Total (without water)72,8804
Polymers72,8804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area7190 Å2
ΔGint-43 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.550, 88.550, 92.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 3 through 152)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 3 - 152 / Label seq-ID: 3 - 152

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 3 through 152)AA
2chain BBB

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Components

#1: Protein 101015D


Mass: 18220.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia tenerifensis NBRC 101015 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.48 Å3/Da / Density % sol: 54.94 %
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 for StmD and 101015DA crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.62→31.94 Å / Num. obs: 47357 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 12.35 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.056 / Rrim(I) all: 0.152 / Net I/σ(I): 9.2 / Num. measured all: 335848 / Scaling rejects: 266
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
1.62-1.657.50.311713922970.930.120.3335100
8.86-31.9470.1124973560.9720.0420.11812.798.2

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Processing

Software
NameVersionClassification
Aimless0.6.3data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A5F

6a5f


Resolution: 1.618→31.943 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 2009 4.25 %
Rwork0.1744 45315 -
obs0.1755 47324 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.91 Å2 / Biso mean: 17.9613 Å2 / Biso min: 2.67 Å2
Refinement stepCycle: final / Resolution: 1.618→31.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 0 421 2752
Biso mean---33.15 -
Num. residues----301
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1388X-RAY DIFFRACTION5.063TORSIONAL
12B1388X-RAY DIFFRACTION5.063TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.618-1.65850.23251430.212331613304
1.6585-1.70330.2161370.196932163353
1.7033-1.75340.24071410.189431533294
1.7534-1.810.24021420.19132043346
1.81-1.87470.2081390.178731943333
1.8747-1.94970.21431470.17931973344
1.9497-2.03850.20361420.17531943336
2.0385-2.14590.20521350.175532183353
2.1459-2.28030.21051520.175532193371
2.2803-2.45630.20151400.175832423382
2.4563-2.70340.19151420.173532363378
2.7034-3.09430.18651500.169132683418
3.0943-3.89740.17511460.155833253471
3.8974-31.9490.19791530.173434883641
Refinement TLS params.Method: refined / Origin x: -28.3588 Å / Origin y: -3.5577 Å / Origin z: 0.7587 Å
111213212223313233
T0.0207 Å20.0126 Å20.0018 Å2-0.0678 Å2-0.0094 Å2--0.042 Å2
L0.1321 °2-0.0847 °20.0792 °2-0.2139 °20.1133 °2--0.5089 °2
S-0.0718 Å °0.0059 Å °0.0158 Å °0.0387 Å °0.107 Å °-0.0693 Å °-0.0524 Å °0.2452 Å °0.0282 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 152
2X-RAY DIFFRACTION1allB3 - 152

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