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- PDB-6f9q: Binary complex of a 7S-cis-cis-nepetalactol cyclase from Nepeta m... -

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Basic information

Entry
Database: PDB / ID: 6f9q
TitleBinary complex of a 7S-cis-cis-nepetalactol cyclase from Nepeta mussinii with NAD+
Components7S-cis-cis-nepetalactol cyclase
KeywordsBIOSYNTHETIC PROTEIN / IRIDOID / NATURAL PRODUCT / BIOSYNTHESIS / SHORT CHAIN DEHYDROGENASE / CYCLASE
Function / homology
Function and homology information


(+)-cis,cis-nepetalactol synthase / isomerase activity / oxidoreductase activity
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (+)-cis,cis-nepetalactol synthase NEPS3
Similarity search - Component
Biological speciesNepeta racemosa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLichman, B.R. / Kamileen, M.O. / Titchiner, G. / Saalbach, G. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1444499 United States
Biotechnology and Biological Sciences Research CouncilBB/L014130/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012523/1 United Kingdom
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Uncoupled activation and cyclization in catmint reductive terpenoid biosynthesis.
Authors: Lichman, B.R. / Kamileen, M.O. / Titchiner, G.R. / Saalbach, G. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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
A: 7S-cis-cis-nepetalactol cyclase
B: 7S-cis-cis-nepetalactol cyclase
C: 7S-cis-cis-nepetalactol cyclase
D: 7S-cis-cis-nepetalactol cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,24612
Polymers113,4514
Non-polymers2,7968
Water18,9161050
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18390 Å2
ΔGint-188 kcal/mol
Surface area31780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.921, 107.750, 69.361
Angle α, β, γ (deg.)90.000, 104.260, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA9 - 26511 - 267
21PHEPHEBB9 - 26511 - 267
12PROPROAA9 - 26411 - 266
22PROPROCC9 - 26411 - 266
13PROPROAA9 - 26411 - 266
23PROPRODD9 - 26411 - 266
14PROPROBB9 - 26411 - 266
24PROPROCC9 - 26411 - 266
15PROPROBB9 - 26411 - 266
25PROPRODD9 - 26411 - 266
16PHEPHECC9 - 26511 - 267
26PHEPHEDD9 - 26511 - 267

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
7S-cis-cis-nepetalactol cyclase


Mass: 28362.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The source organism is alos referred to as Nepeta racemosa with taxonomy ID 54731
Source: (gene. exp.) Nepeta racemosa (plant) / Plasmid: POPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SOLU
References: UniProt: A0A3Q8GLE8*PLUS, Isomerases; Intramolecular transferases; Transferring other groups
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1050 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: NULL / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→47.16 Å / Num. obs: 175909 / % possible obs: 98.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.4-1.426.91.56486100.5610.6371.6997
7.67-47.166.40.03611220.9980.0150.03999.2

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Processing

Software
NameVersionClassification
XDS2016-11-01data reduction
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BGK

2bgk


Resolution: 1.4→47.16 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.272 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1682 8822 5 %RANDOM
Rwork0.1505 ---
obs0.1513 167049 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.15 Å2 / Biso mean: 18.4 Å2 / Biso min: 10.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20.02 Å2
2---0.33 Å20 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.4→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7529 0 184 1109 8822
Biso mean--14.56 30.52 -
Num. residues----1032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198407
X-RAY DIFFRACTIONr_bond_other_d0.0020.0197982
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.98411458
X-RAY DIFFRACTIONr_angle_other_deg0.945318510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60151144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.91927.167240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61151242
X-RAY DIFFRACTIONr_chiral_restr0.0880.21323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029640
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021762
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A167060.05
12B167060.05
21A165840.05
22C165840.05
31A166360.05
32D166360.05
41B166560.05
42C166560.05
51B167600.04
52D167600.04
61C166720.06
62D166720.06
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 614 -
Rwork0.276 12207 -
all-12821 -
obs--96.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
117.56273.1818-0.18782.58812.61473.61270.0717-0.9139-0.40730.4386-0.18270.03340.3711-0.12210.1110.39870.13170.05570.19290.05220.1425.159-16.82111.246
21.09170.2282-0.1061.7668-0.7061.52380.0293-0.13280.02790.20990.0407-0.1146-0.1160.1016-0.070.05640.0042-0.01390.0354-0.01680.021314.529-3.3065.047
30.5233-0.02680.03751.121-0.11420.7084-0.01280.00630.02890.00540.03780.0173-0.09170.0058-0.0250.0371-0.00920.00690.034-0.00070.00366.714-2.36-10.726
41.3262-0.6341-0.12350.97360.23220.71730.01570.01780.1087-0.0464-0.0220.02-0.1089-0.05670.00630.0467-0.00880.00460.02-0.00270.0186-6.902-5.169-3.937
52.41320.122-0.34053.17462.07063.58420.0385-0.24320.00230.34320.058-0.16180.04810.1781-0.09650.09590.00240.00270.03860.0060.0236-10.65-25.826.946
61.222-0.57490.14892.7485-0.0481.0473-0.0212-0.1599-0.19070.41660.12320.20860.1555-0.15-0.1020.1287-0.00380.03580.03920.04080.0578-20.542-33.7894.607
70.31410.1440.04410.80680.16681.0152-0.00210.0053-0.00890.02510.0020.0410.0796-0.04010.00010.01990.00360.00650.0110.00710.0083-17.843-24.403-9.353
81.2711-0.6263-0.42811.08430.0940.52440.0020.0434-0.1128-0.0683-0.0242-0.00890.12770.02810.02220.05960.0087-0.00070.0212-0.00240.0194-0.82-28.066-8.121
913.92698.34692.02768.3147-3.28529.4577-0.74240.34351.5369-0.53840.66230.8274-1.1615-0.50340.08010.5093-0.02250.02230.15690.0090.1983-12.205-12.746-52.114
100.38250.1408-0.0440.5231-0.07551.90190.00910.0802-0.0502-0.09170.01530.07220.1138-0.1669-0.02430.0525-0.0018-0.01390.0455-0.00480.0286-24.396-23.791-37.668
111.3486-0.1656-0.54030.81780.17190.94080.04880.06880.0848-0.0478-0.01940.0363-0.032-0.1051-0.02940.0467-0.00010.00280.02670.00510.0083-17.842-16.597-28.918
120.6341-0.7255-0.19652.1780.58271.213-0.0176-0.01960.03070.07140.00830.113-0.1047-0.12960.00930.04120.0040.0090.04730.01020.0233-16.233-5.833-31.515
131.9531-4.23853.253428.0674-5.12995.68120.10410.0904-0.164-1.33140.12590.80090.0992-0.0221-0.230.16-0.1285-0.00640.66780.01120.0785-6.851-1.54-50.826
140.7240.0560.13940.3667-0.18691.03840.01680.0480.0264-0.05260.0135-0.0336-0.0550.0899-0.03040.069-0.00790.02460.03250.00040.01227.0950.72-35.308
1511.20458.5876-0.78847.4020.112.3458-0.34130.9523-0.7245-0.35980.4533-0.767-0.05130.0684-0.11210.13410.06170.04970.28350.00840.179615.061-21.384-35.483
160.7893-0.4976-0.20272.39250.06721.1623-0.0029-0.022-0.0348-0.0168-0.0109-0.14620.09260.09670.01380.0492-0.00550.01530.02680.00530.0227-0.173-14.041-35.716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 13
2X-RAY DIFFRACTION2A14 - 93
3X-RAY DIFFRACTION3A94 - 212
4X-RAY DIFFRACTION4A213 - 265
5X-RAY DIFFRACTION5B9 - 39
6X-RAY DIFFRACTION6B40 - 78
7X-RAY DIFFRACTION7B79 - 196
8X-RAY DIFFRACTION8B197 - 265
9X-RAY DIFFRACTION9C7 - 14
10X-RAY DIFFRACTION10C15 - 142
11X-RAY DIFFRACTION11C143 - 213
12X-RAY DIFFRACTION12C214 - 266
13X-RAY DIFFRACTION13D9 - 14
14X-RAY DIFFRACTION14D15 - 203
15X-RAY DIFFRACTION15D204 - 221
16X-RAY DIFFRACTION16D222 - 266

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