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- PDB-3ie5: Crystal structure of Hyp-1 protein from Hypericum perforatum (St ... -

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Basic information

Entry
Database: PDB / ID: 3ie5
TitleCrystal structure of Hyp-1 protein from Hypericum perforatum (St John's wort) involved in hypericin biosynthesis
ComponentsPhenolic oxidative coupling protein Hyp-1
KeywordsPlant Protein / BIOSYNTHETIC PROTEIN / hypericin / St John's wort / depression / allergy / PR-10 protein / cytokinin / plant hormones / polyethylene glycol / PEG / Pathogenesis-related protein / Plant defense
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Phenolic oxidative coupling protein
Similarity search - Component
Biological speciesHypericum perforatum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.688 Å
AuthorsMichalska, K. / Fernandes, H. / Sikorski, M.M. / Jaskolski, M.
Citation
Journal: J.Struct.Biol. / Year: 2010
Title: Crystal structure of Hyp-1, a St. John's wort protein implicated in the biosynthesis of hypericin
Authors: Michalska, K. / Fernandes, H. / Sikorski, M.M. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary crystallographic studies of Hyp-1, a St John's wort protein implicated in the biosynthesis of hypericin
Authors: Fernandes, H. / Konieczna, M. / Kolodziejczyk, R. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#2: Journal: Febs J. / Year: 2009
Title: Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein
Authors: Fernandes, H. / Bujacz, A. / Bujacz, G. / Jelen, F. / Jasinski, M. / Kachlicki, P. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#3: Journal: J.Mol.Biol. / Year: 2008
Title: Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin
Authors: Fernandes, H. / Pasternak, O. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M.
#4: Journal: Plant Cell / Year: 2006
Title: Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin
Authors: Pasternak, O. / Bujacz, G.D. / Fujimoto, Y. / Hashimoto, Y. / Jelen, F. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass
Authors: Pasternak, O. / Biesiadka, J. / Dolot, R. / Handschuh, L. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#6: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine
Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#7: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy
Authors: Gajhede, M. / Osmark, P. / Poulsen, F.M. / Ipsen, H. / Larsen, J.N. / Joost van Neerven, R.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenolic oxidative coupling protein Hyp-1
B: Phenolic oxidative coupling protein Hyp-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,10013
Polymers36,9902
Non-polymers2,11011
Water4,648258
1
A: Phenolic oxidative coupling protein Hyp-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6347
Polymers18,4951
Non-polymers1,1396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenolic oxidative coupling protein Hyp-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4666
Polymers18,4951
Non-polymers9715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.538, 76.713, 119.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phenolic oxidative coupling protein Hyp-1


Mass: 18495.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypericum perforatum (plant) / Gene: hyp-1 / Plasmid: pET151/D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8H1L1

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Non-polymers , 7 types, 269 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE RESIDUES ARE NUMBERED NON-SEQUENTIALLY. RESIDUE NUMBER ZERO IS SIMPLY SKIPPED IN THE NUMBERING, ...THE RESIDUES ARE NUMBERED NON-SEQUENTIALLY. RESIDUE NUMBER ZERO IS SIMPLY SKIPPED IN THE NUMBERING, TO SEPARATE THE HIS-TAG SEQUENCE FROM THE GENUINE PROTEIN SEQUENCE. THE AMINO ACID SEQUENCE OF THE PRESENT PROTEIN DIFFERS FROM THE DEPOSITED SEQUENCE Q8H1L1 POSSIBLY BECAUSE OF GENETIC VARIABILITY.

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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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.4M NaCl, 0.1M Tris/HCl, 30% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2008 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.688→30 Å / Num. all: 39813 / Num. obs: 39813 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 20.58 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.4
Reflection shellResolution: 1.688→1.75 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3912 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0

1xdf

2qim

2flh

1tw0

2bk0


Resolution: 1.688→27.663 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.39 / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 1.34 / Phase error: 18.42 / Stereochemistry target values: Engh & Huber / Details: Hydrogen atoms were added at riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1590 4 %random
Rwork0.17 38152 --
all0.172 39742 --
obs0.172 39742 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.754 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso max: 115.59 Å2 / Biso mean: 27.532 Å2 / Biso min: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1-4.8754 Å20 Å20 Å2
2--4.6346 Å20 Å2
3----9.51 Å2
Refine analyzeLuzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 1.688→27.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 140 258 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152950
X-RAY DIFFRACTIONf_angle_d1.5253966
X-RAY DIFFRACTIONf_chiral_restr0.11421
X-RAY DIFFRACTIONf_plane_restr0.007505
X-RAY DIFFRACTIONf_dihedral_angle_d18.8461159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6883-1.74860.25161580.22723715404999
1.7486-1.81860.21611650.20137713867100
1.8186-1.90140.20271390.173337643849100
1.9014-2.00160.19831700.162137533815100
2.0016-2.1270.20591400.15437943775100
2.127-2.29110.21881780.150137753794100
2.2911-2.52160.20821600.154938153753100
2.5216-2.88610.18811540.167338493764100
2.8861-3.63490.21071480.16838673771100
3.6349-27.66640.19241780.167640493715100
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)
10.61310.49790.21311.00061.55172.23680.21290.0564-0.19210.5288-0.1032-0.66070.5951-0.1796-0.16410.183-0.01420.00030.05390.01140.2728-1.8774-6.2398.2202
20.8137-0.0327-0.41670.4426-0.4131.2131-0.12720.12930.14010.06140.04030.1774-0.1646-0.0660.09350.0249-0.02730.01110.0762-0.01860.2041-1.675813.15498.7553
30.80860.8143-0.31540.9875-0.36990.0557-0.08180.1088-0.0503-0.06960.16090.01550.08680.0143-0.04670.067-0.00540.02730.2006-0.06150.21699.078311.63593.239
40.82060.6319-0.05290.62980.21141.1404-0.01550.1276-0.01750.04060.0201-0.11070.0158-0.025-0.00580.00330.0140.00130.02540.0070.19343.09342.1975-1.8765
5-0.071-1.0278-0.01173.77121.42181.196-0.04670.0336-0.045-0.03150.3383-0.08790.05240.3429-0.26170.05680.010.00050.1211-0.040.26757.38763.849210.218
60.57440.09770.0771-1.0020.2483.1623-0.25290.09320.0571-0.0107-0.12250.1708-0.089-0.38210.28930.27660.0073-0.05450.10370.00930.2656-4.1822-4.768616.4997
71.31580.77240.9980.64720.03121.3395-0.18990.08050.0922-0.03190.1403-0.1147-0.14690.11010.08040.0556-0.0035-0.01920.0387-0.00490.22874.3662-5.78336.8853
81.2340.3751-0.38850.8917-0.42390.5407-0.09130.003-0.0914-0.11590.118-0.0620.0531-0.0253-0.01670.10140.002-0.00670.12960.02450.2634-5.015-14.849536.86
90.6572-0.30820.20070.42770.14091.6178-0.1455-0.026-0.0648-0.23010.0819-0.10070.0329-0.05370.04360.0759-0.00120.00650.03080.01150.2029-0.9334-16.257825.991
101.1781-0.31681.10070.6751-0.1561.4880.0526-0.1776-0.0803-0.1013-0.01750.12720.0253-0.302-0.04310.06040.0187-0.04730.04130.00620.1815-7.3384-5.582531.5234
116.0777-2.14812.09674.29313.0755.0151-0.1010.8733-0.08013.79141.02170.9914-3.0574-0.719-0.99060.8733-0.3214-0.0840.60590.00280.62021.6944-1.112.1332
123.18082.81376.94142.7542.03373.35140.5205-0.6189-1.25720.32120.02653.61170.1123-0.2836-0.50310.3374-0.23790.24410.3766-0.04470.92728.5848-1.00522.2495
134.77055.91080.389225.55710.2018-0.38-0.1704-0.05120.0684-0.1535-0.11240.0487-0.17540.45450.58390.0681-0.02670.41810.0110.3231-2.1781-6.190328.3178
143.2606-0.534-4.52547.9993-2.6175.1729-0.3359-0.3075-0.15690.0528-0.08520.4580.12010.67650.37640.3808-0.0071-0.00550.42120.41370.9736-10.7087-14.931724.8922
158.2988-2.5733.67745.42987.85865.8069-0.5452-1.0641-1.2665-0.4322-0.1169-0.33340.19150.42410.63921.1551-0.3152-0.27660.35320.23690.4673-9.5849-12.012629.6493
168.4589-2.13093.58964.93770.94892.3907-0.1650.5337-1.0407-0.0439-0.49140.08360.4701-0.16340.52550.4228-0.04470.07110.3943-0.14290.6291-2.7911-11.621342.4693
17-0.75460.4944-0.2974-0.101-0.5925-0.16060.18520.01240.114-0.11280.1731-0.0465-0.02550.0776-0.31150.5271-0.098-0.01010.636-0.08820.834211.460720.04553.7307
186.6445-2.5852-1.44023.8004-4.21373.88990.11840.154-0.04680.0137-0.0471-0.12020.03350.0974-0.02420.52660.1721-0.08420.4733-0.14920.4853-1.26483.796-13.7189
195.78544.04972.0012.0099-0.94521.9911-0.11910.00480.0313-0.84950.130.01921.0888-0.1455-0.01710.85560.0980.31940.6323-0.11141.55482.6034-20.479414.5714
201.88550.0511-0.05260.42080.43121.0541-0.1011-0.00230.1974-0.0358-0.18470.32640.0282-0.26580.24560.5487-0.31510.00131.2418-0.22780.722-4.2664-6.4365-9.1377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resi -1:13A0
2X-RAY DIFFRACTION2chain A and resi 14:24A0
3X-RAY DIFFRACTION3chain A and resi 25:37A0
4X-RAY DIFFRACTION4chain A and resi 38:127A0
5X-RAY DIFFRACTION5chain A and resi 128:159A0
6X-RAY DIFFRACTION6chain B and resi -5:13B0
7X-RAY DIFFRACTION7chain B and resi 14:24B0
8X-RAY DIFFRACTION8chain B and resi 25:37B0
9X-RAY DIFFRACTION9chain B and resi 38:127B0
10X-RAY DIFFRACTION10chain B and resi 128:159B0
11X-RAY DIFFRACTION11chain A and resi 501A - D0
12X-RAY DIFFRACTION12chain A and resi 502A - E0
13X-RAY DIFFRACTION13chain B and resi 503B - F0
14X-RAY DIFFRACTION14chain B and resi 504B - G0
15X-RAY DIFFRACTION15chain B and resi 505B - H0
16X-RAY DIFFRACTION16chain B and resi 506B - I0
17X-RAY DIFFRACTION17chain A and resi 507A - J0
18X-RAY DIFFRACTION18chain A and resi 508A - K0
19X-RAY DIFFRACTION19chain A and resi 509B - L0
20X-RAY DIFFRACTION20chain B and resi 510A - M0

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