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- PDB-5nx5: Crystal structure of Linalool/Nerolidol synthase from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 5nx5
TitleCrystal structure of Linalool/Nerolidol synthase from Streptomyces clavuligerus in complex with 2-fluorogeranyl diphosphate
ComponentsPentalenene synthase
KeywordsLIGASE / terpene synthase / linalool / nerolidol / monoterpenoid
Function / homology
Function and homology information


R-linalool synthase / R-linalool synthase activity / geranyl diphosphate metabolic process / farnesyl diphosphate metabolic process / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0FV / PHOSPHATE ION / R-linalool synthase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsKaruppiah, V. / Leys, D. / Scrutton, N.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M000354/1 United Kingdom
CitationJournal: ACS Catal / Year: 2017
Title: Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.
Authors: Karuppiah, V. / Ranaghan, K.E. / Leferink, N.G.H. / Johannissen, L.O. / Shanmugam, M. / Ni Cheallaigh, A. / Bennett, N.J. / Kearsey, L.J. / Takano, E. / Gardiner, J.M. / van der Kamp, M.W. / ...Authors: Karuppiah, V. / Ranaghan, K.E. / Leferink, N.G.H. / Johannissen, L.O. / Shanmugam, M. / Ni Cheallaigh, A. / Bennett, N.J. / Kearsey, L.J. / Takano, E. / Gardiner, J.M. / van der Kamp, M.W. / Hay, S. / Mulholland, A.J. / Leys, D. / Scrutton, N.S.
History
DepositionMay 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pentalenene synthase
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,88312
Polymers72,9002
Non-polymers98310
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-48 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.370, 139.370, 86.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pentalenene synthase / / Linalool/Nerolidol synthase


Mass: 36450.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_p1185 / Production host: Escherichia coli (E. coli) / References: UniProt: D5SL78, pentalenene synthase

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Non-polymers , 6 types, 524 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0FV / (2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate / 2-fluorogeranyl diphosphate


Mass: 332.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H19FO7P2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Alcohols (0.2M 1,6-hexanediol, 0.2M 1-nutanol, 0.2M 1,2-propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol), 0.1 M Buffer System 2 (1.0M sodium HEPES, MOPS (acid)) ...Details: 0.12 M Alcohols (0.2M 1,6-hexanediol, 0.2M 1-nutanol, 0.2M 1,2-propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol), 0.1 M Buffer System 2 (1.0M sodium HEPES, MOPS (acid)) pH 7.5 and 50 % v/v precipitant Mix 3 (40% v/v glycerol, 20% w/v PEG 4000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.82→36.62 Å / Num. obs: 73739 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Net I/σ(I): 18.2
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3654 / CC1/2: 0.51 / Rpim(I) all: 0.563 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2621: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PS1
Resolution: 1.82→34.843 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.24
RfactorNum. reflection% reflection
Rfree0.1889 3550 4.81 %
Rwork0.1667 --
obs0.1678 73730 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.82→34.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 58 514 4990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094615
X-RAY DIFFRACTIONf_angle_d0.946263
X-RAY DIFFRACTIONf_dihedral_angle_d9.9162669
X-RAY DIFFRACTIONf_chiral_restr0.049665
X-RAY DIFFRACTIONf_plane_restr0.007816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.8450.34381650.29142797X-RAY DIFFRACTION100
1.845-1.87130.31221150.26892782X-RAY DIFFRACTION100
1.8713-1.89920.27871280.26292786X-RAY DIFFRACTION100
1.8992-1.92890.28981380.24162799X-RAY DIFFRACTION100
1.9289-1.96050.26791450.21842812X-RAY DIFFRACTION100
1.9605-1.99430.21641220.20532826X-RAY DIFFRACTION100
1.9943-2.03060.20891460.19692798X-RAY DIFFRACTION100
2.0306-2.06970.22971400.19042801X-RAY DIFFRACTION100
2.0697-2.11190.21941320.18522823X-RAY DIFFRACTION100
2.1119-2.15780.22631450.16972775X-RAY DIFFRACTION100
2.1578-2.2080.19081180.16592820X-RAY DIFFRACTION100
2.208-2.26320.17121570.162782X-RAY DIFFRACTION100
2.2632-2.32440.17911390.15012796X-RAY DIFFRACTION100
2.3244-2.39280.16051490.14852815X-RAY DIFFRACTION100
2.3928-2.470.18411670.15232758X-RAY DIFFRACTION100
2.47-2.55820.18371530.15252815X-RAY DIFFRACTION100
2.5582-2.66060.21941350.16092799X-RAY DIFFRACTION100
2.6606-2.78170.18541420.14862815X-RAY DIFFRACTION100
2.7817-2.92830.18741330.15642798X-RAY DIFFRACTION100
2.9283-3.11160.16111210.15292845X-RAY DIFFRACTION100
3.1116-3.35170.1651650.15222806X-RAY DIFFRACTION100
3.3517-3.68860.19061530.14232804X-RAY DIFFRACTION100
3.6886-4.22160.15251680.13932792X-RAY DIFFRACTION100
4.2216-5.31570.15861200.15412867X-RAY DIFFRACTION100
5.3157-34.84890.22861540.21672869X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.4211.4235-4.03457.7246-2.4472.551-0.0835-0.5781-0.47760.544-0.1099-0.02180.09330.2920.21220.28950.0057-0.00610.37120.08750.2492-23.3684-32.4366-10.5895
23.1714-1.6412-2.54684.88261.25035.1474-0.1199-0.1717-0.33260.46110.11560.41810.6864-0.19920.19920.3229-0.0370.00940.26980.0320.3761-30.1443-34.8053-20.8235
36.6296-3.073-2.76833.18222.4485.2389-0.0203-0.35460.07170.26170.02080.0352-0.1631-0.13020.00950.2756-0.02110.02570.28310.01690.2313-26.9525-24.8247-16.8728
42.5392-1.8055-0.20385.19071.8945.2283-0.0012-0.25430.390.34090.0297-0.3969-0.28570.278-0.08090.2314-0.0788-0.00320.2884-0.03290.2967-20.9357-14.2506-19.1941
52.6859-1.5592-0.40722.21050.82591.02230.1033-0.03670.11670.16240.03280.0411-0.1568-0.0657-0.1480.3269-0.01160.03770.23580.01150.2819-36.2962-13.0051-21.7141
63.796-1.6661.5012.4662-0.35413.17860.03390.3404-0.0737-0.2164-0.08730.00920.04130.17560.01860.2744-0.0362-0.00520.2618-0.0240.2723-29.5738-23.0377-35.3159
74.6907-0.7454-3.7173.34350.39266.5037-0.0223-0.6025-0.21990.57780.0430.41620.08120.2757-0.04290.2634-0.04540.04250.23720.01960.3136-47.0141-20.9964-19.3309
86.4230.1924-5.08791.0093-0.07634.27090.01990.4488-0.1395-0.0723-0.04710.3848-0.0705-0.75420.14820.2707-0.0203-0.02290.3001-0.0250.3443-48.2836-26.7013-33.3633
93.73310.4997-1.71213.9474-3.1713.2123-0.0246-0.0491-0.3273-0.00750.09210.13540.4238-0.1688-0.060.3141-0.022-0.03120.2763-0.03590.3898-35.9273-31.8822-31.784
105.38920.5267-0.46253.6317-0.53781.8544-0.14880.62220.1068-0.40140.09240.4982-0.1948-0.31110.10170.4644-0.0476-0.12290.3820.01290.3528-40.704214.4923-40.7936
116.00780.0810.39229.76382.70044.8548-0.25610.6014-0.415-0.715-0.03450.43220.173-0.240.18540.3669-0.08210.00620.2983-0.01760.2687-34.87827.8909-40.6756
123.1522-1.311-1.88617.39852.22365.8948-0.11040.3669-0.186-0.4419-0.013-0.51830.02230.16680.05820.2673-0.05490.06780.2984-0.01890.3147-24.5981.6368-37.3765
131.2711.26891.79935.12163.26954.0655-0.11350.152-0.0126-0.2940.1504-0.0527-0.18630.16590.06690.3229-0.02440.0570.27560.00570.2965-33.092-4.9119-33.9572
141.62541.45850.77737.40182.61422.4632-0.08430.1802-0.189-0.40920.12650.11980.05450.4965-0.02940.42910.06580.01780.40.01980.3182-44.8219-10.0552-38.8251
152.4322.1011-0.44847.6725-0.12222.9729-0.11450.01770.01520.40210.02710.1308-0.00290.01770.09420.27980.00860.03850.2451-0.0150.305-37.54724.9214-22.5124
163.43740.60822.68215.2892.59987.1055-0.0590.38460.009-0.789-0.13320.3775-0.2142-0.1320.17520.33660.02180.00880.28010.00330.3716-50.9363-5.4439-39.325
174.06471.15424.00533.22233.13658.77010.0727-0.2610.04230.2829-0.34780.8650.3615-0.94740.22060.3477-0.00710.10370.37020.00130.5521-55.4993-1.5153-25.3113
183.88290.45912.89134.4311.20687.8658-0.06590.28110.1965-0.27770.12920.4831-0.0352-0.19670.12560.33150.02110.02060.32760.00680.4986-47.63998.5723-29.8789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 132 )
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 200 )
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 245 )
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 278 )
9X-RAY DIFFRACTION9chain 'A' and (resid 279 through 304 )
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 82 )
12X-RAY DIFFRACTION12chain 'B' and (resid 83 through 132 )
13X-RAY DIFFRACTION13chain 'B' and (resid 133 through 159 )
14X-RAY DIFFRACTION14chain 'B' and (resid 160 through 177 )
15X-RAY DIFFRACTION15chain 'B' and (resid 178 through 200 )
16X-RAY DIFFRACTION16chain 'B' and (resid 201 through 245 )
17X-RAY DIFFRACTION17chain 'B' and (resid 246 through 278 )
18X-RAY DIFFRACTION18chain 'B' and (resid 279 through 309 )

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