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- PDB-6a5f: The structure of [4+2] and [6+4] cyclase in the biosynthetic path... -

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Basic information

Entry
Database: PDB / ID: 6a5f
TitleThe structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of nargenicin
ComponentsNgnD
KeywordsBIOSYNTHETIC PROTEIN / nargenicin / biosynthesis
Biological speciesNocardia argentinensis ATCC 31306 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: NgnD
B: NgnD


Theoretical massNumber of molelcules
Total (without water)36,1882
Polymers36,1882
Non-polymers00
Water4,089227
1
A: NgnD

B: NgnD


Theoretical massNumber of molelcules
Total (without water)36,1882
Polymers36,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area1900 Å2
ΔGint-17 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.990, 116.990, 63.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 2 - 152 / Label seq-ID: 2 - 152

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein NgnD


Mass: 18093.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia argentinensis ATCC 31306 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.43 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM sodium citrate, pH 4.2, 40% v/v ethanol, 5% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
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: 2.05→23.08 Å / Num. obs: 31359 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.66 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.066 / Rrim(I) all: 0.177 / Net I/σ(I): 6.6 / Num. measured all: 199240 / Scaling rejects: 204
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
2.05-2.115.10.9751238424050.5260.4551.0821.699.2
8.94-23.088.10.08732264000.9950.0310.0931494

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.24data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→23.078 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1843 2002 6.39 %
Rwork0.1592 29332 -
obs0.1608 31334 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.01 Å2 / Biso mean: 36.4403 Å2 / Biso min: 14.64 Å2
Refinement stepCycle: final / Resolution: 2.05→23.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 0 227 2543
Biso mean---45.39 -
Num. residues----302
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1373X-RAY DIFFRACTION14.252TORSIONAL
12B1373X-RAY DIFFRACTION14.252TORSIONAL
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 (%)
2.0501-2.10130.28291430.26822063220699
2.1013-2.15810.29691400.24262024216498
2.1581-2.22150.2691360.22232051218798
2.2215-2.29320.22181470.20172083223099
2.2932-2.37510.22011400.18092063220399
2.3751-2.47010.21781420.179420852227100
2.4701-2.58230.19761440.180420662210100
2.5823-2.71830.18821430.164621402283100
2.7183-2.88830.21331350.16752070220599
2.8883-3.11080.18521400.165221002240100
3.1108-3.4230.20661440.157921292273100
3.423-3.91620.15781490.144221282277100
3.9162-4.92610.13131460.115621282274100
4.9261-23.07960.15281530.135822022355100
Refinement TLS params.Method: refined / Origin x: 26.229 Å / Origin y: -39.1935 Å / Origin z: 10.1232 Å
111213212223313233
T0.1947 Å2-0.0109 Å2-0.0178 Å2-0.2104 Å20.0275 Å2--0.1821 Å2
L1.6479 °20.9112 °2-0.1713 °2-0.7211 °2-0.1097 °2--0.3959 °2
S-0.1699 Å °0.2865 Å °0.1362 Å °-0.1937 Å °0.1754 Å °0.0793 Å °-0.0056 Å °-0.1029 Å °0.0462 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 152
2X-RAY DIFFRACTION1allB2 - 152
3X-RAY DIFFRACTION1allS1 - 227

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