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- PDB-5ajt: Crystal structure of ligand-free phosphoribohydrolase lonely guy ... -

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Basic information

Entry
Database: PDB / ID: 5ajt
TitleCrystal structure of ligand-free phosphoribohydrolase lonely guy from Claviceps purpurea
ComponentsPHOSPHORIBOHYDROLASE LONELY GUY
KeywordsHYDROLASE / CYTOKININ / ROSSMANN FOLD / LYSINE DECARBOXYLASE
Function / homology
Function and homology information


hydrolase activity, hydrolyzing N-glycosyl compounds / cytokinin biosynthetic process / cytosol
Similarity search - Function
Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Rossmann fold nucleotide-binding protein
Similarity search - Component
Biological speciesCLAVICEPS PURPUREA (ergot fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsDzurova, L. / Savino, S. / Forneris, F.
CitationJournal: Proteins / Year: 2015
Title: The three-dimensional structure of "Lonely Guy" from Claviceps purpurea provides insights into the phosphoribohydrolase function of Rossmann fold-containing lysine decarboxylase-like proteins.
Authors: Dzurova, L. / Forneris, F. / Savino, S. / Galuszka, P. / Vrabka, J. / Frebort, I.
History
DepositionFeb 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 2.0Jun 26, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / entity / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_biol
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_auth_atom_name / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.identifier_ORCID / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PHOSPHORIBOHYDROLASE LONELY GUY
B: PHOSPHORIBOHYDROLASE LONELY GUY
C: PHOSPHORIBOHYDROLASE LONELY GUY
D: PHOSPHORIBOHYDROLASE LONELY GUY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,74914
Polymers116,6884
Non-polymers1,06110
Water2,324129
1
A: PHOSPHORIBOHYDROLASE LONELY GUY
B: PHOSPHORIBOHYDROLASE LONELY GUY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8307
Polymers58,3442
Non-polymers4865
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-21 kcal/mol
Surface area18820 Å2
MethodPISA
2
C: PHOSPHORIBOHYDROLASE LONELY GUY
D: PHOSPHORIBOHYDROLASE LONELY GUY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9187
Polymers58,3442
Non-polymers5745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-17.7 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.540, 83.170, 163.652
Angle α, β, γ (deg.)90.00, 94.03, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
PHOSPHORIBOHYDROLASE LONELY GUY


Mass: 29171.932 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLAVICEPS PURPUREA (ergot fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1VUY5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.42 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100MM AMMONIUM TARTRATE, 100MM POTASSIUM SULFATE, 23% PEG3350, 17% GLYCEROL, 3% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.43→46.47 Å / Num. obs: 41288 / % possible obs: 98.9 % / Observed criterion σ(I): 1.5 / Redundancy: 3 % / Biso Wilson estimate: 54.69 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 2.43→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A33

2a33


Resolution: 2.43→46.471 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 32.02 / Stereochemistry target values: ML
Details: RESIDUES VISIBLE IN THE ELECTRON DENSITY RANGING FROM 24 TO 240
RfactorNum. reflection% reflection
Rfree0.2401 1937 4.7 %
Rwork0.2151 --
obs0.2163 41189 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67 Å2
Refinement stepCycle: LAST / Resolution: 2.43→46.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 70 129 6743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046867
X-RAY DIFFRACTIONf_angle_d1.1149316
X-RAY DIFFRACTIONf_dihedral_angle_d16.1092517
X-RAY DIFFRACTIONf_chiral_restr0.0351036
X-RAY DIFFRACTIONf_plane_restr0.0041219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.49080.45951380.37882778X-RAY DIFFRACTION99
2.4908-2.55810.38091470.36282800X-RAY DIFFRACTION99
2.5581-2.63340.33951510.3252766X-RAY DIFFRACTION99
2.6334-2.71840.38181300.322799X-RAY DIFFRACTION98
2.7184-2.81550.36961350.3072728X-RAY DIFFRACTION97
2.8155-2.92820.35571470.30012807X-RAY DIFFRACTION99
2.9282-3.06150.3511410.28152813X-RAY DIFFRACTION99
3.0615-3.22280.27071390.26572774X-RAY DIFFRACTION99
3.2228-3.42470.24761380.25272793X-RAY DIFFRACTION98
3.4247-3.6890.21871210.21652828X-RAY DIFFRACTION99
3.689-4.06010.1861450.19072822X-RAY DIFFRACTION99
4.0601-4.64710.1981050.1632849X-RAY DIFFRACTION98
4.6471-5.8530.20861610.16732832X-RAY DIFFRACTION99
5.853-46.47930.17931390.16192863X-RAY DIFFRACTION98
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)
10.5908-0.13930.21420.82060.55530.7435-0.24260.12870.46460.44160.3489-0.367-0.40160.0358-0.05590.4946-0.0587-0.08490.7152-0.0430.521215.843640.697478.9666
23.6892-0.6047-1.23820.09930.25830.56260.2591-0.29211.3223-0.64390.11220.053-1.19580.61320.00160.6744-0.0612-0.00730.64220.21580.571717.795647.494471.7614
30.62370.58020.19490.645-0.26861.28080.0790.19440.6302-0.0442-0.1678-0.0823-0.08060.04740.00020.45-0.1004-0.10580.51840.04960.562618.835745.247984.1446
40.2213-0.369-0.00560.52110.01410.29150.23970.6148-0.27770.294-0.2127-0.28540.39740.49240.00080.473-0.1385-0.08830.6561-0.04340.509630.060344.050595.4866
50.80660.23430.66690.10580.10490.56740.0775-0.1972-0.2530.2523-0.1790.2259-0.09850.014900.5094-0.0437-0.0460.5264-0.08580.471816.861437.702190.8205
60.6771-0.06340.83970.4121-0.50451.45790.12150.3030.2077-0.09960.10490.22160.0717-0.0575-0.00020.336-0.0435-0.05150.5514-0.06220.407510.294532.375377.0065
72.2322-1.795-0.55361.62720.06430.9265-0.15050.4768-0.9879-0.17430.05540.46120.0156-0.1877-0.03770.3448-0.0134-0.13840.7657-0.22020.36445.238222.815367.7377
80.2953-0.07480.0280.280.26650.31940.15010.8507-0.0674-0.8174-0.26390.9346-0.4058-0.2433-0.0140.4549-0.0779-0.08450.64930.10220.52465.2942.047370.1793
90.1820.0648-0.21410.0964-0.16770.413-0.16740.05870.1151-0.2206-0.16340.4771-0.028-0.15090.00050.37520.01-0.04710.63020.04440.4673-10.616828.885571.9786
100.18190.0984-0.1780.0543-0.12230.17310.0026-0.0465-0.633-0.12560.06110.23490.06910.00890.00020.474-0.03070.0420.676-0.19130.791514.00457.275877.7191
111.45921.9222-1.67422.5158-2.22463.9685-0.47440.0467-0.9732-0.5234-0.1459-0.70180.8556-0.2825-1.3110.4296-0.20480.0840.6843-0.7081.129812.3110.975770.1327
120.13130.09050.16930.79-0.55691.0589-0.3001-0.073-0.76730.0310.08060.72140.1291-0.065200.4021-0.04010.07890.4901-0.14510.99410.68272.656682.581
130.4435-0.0776-0.36280.4833-0.16590.53670.99830.23530.17960.5924-0.55771.48410.4997-0.75480.00370.6572-0.12840.1110.7291-0.13771.1481-1.48073.375893.0888
141.03580.101-0.1090.24790.44090.6891-0.1778-0.0406-0.45520.1791-0.3470.00560.23060.026-0.00240.4571-0.0897-0.0330.5832-0.05220.648612.40039.628489.8216
150.1043-0.19510.21010.3015-0.28151.1429-0.56690.3579-0.77310.28380.22690.077-0.13640.0193-0.00250.3457-0.0396-0.01850.6134-0.14220.631818.996816.469678.6861
161.6679-0.6975-0.94750.7338-0.03440.60680.18180.3847-0.3332-0.0748-0.1593-0.4790.05880.11600.312-0.032-0.00890.717-0.13820.469722.847419.909969.9072
170.65840.4146-0.64780.27270.17161.4493-0.0102-0.4074-0.6865-0.152-0.5076-0.32780.31810.1353-0.0040.38490.0433-0.02020.6232-0.08640.639134.869513.210271.5635
180.7805-0.25160.44251.0056-1.08041.1023-0.1178-0.1449-0.1694-0.00170.0904-0.78940.27850.2319-0.00190.74690.07730.34840.4995-0.00020.789533.285964.0497117.4348
190.8406-0.72160.79570.5681-0.7741.24360.03670.0415-0.1677-0.1769-0.1942-0.61360.40150.35190.00020.62310.07960.24340.48550.04690.882833.180361.54126.1533
200.44460.37330.2340.31180.17070.1332-0.3071-0.2968-0.8394-0.33720.3999-0.2830.32050.42060.00010.65570.19480.26790.70220.16781.068631.725150.1027137.2169
212.00191.27632.92430.32170.45390.89320.3635-1.60350.3832-0.4015-0.5653-0.23330.14960.0942-0.03210.48960.15320.11080.39940.19730.634630.104558.692133.6598
220.58830.40090.02590.9881-0.28571.4953-0.0019-0.0262-0.0053-0.1742-0.1205-0.6133-0.1549-0.213400.70440.07590.12810.36920.03970.443820.624869.2447121.59
231.6420.31450.47010.44860.26490.2532-0.20240.05090.2784-0.9661-0.11220.05330.38740.1019-0.09891.11290.0720.14590.44770.10980.413914.024374.4768108.9083
240.8222-0.5460.05850.9266-0.71751.3244-0.8530.0855-0.09710.20180.3025-0.17880.02550.2954-0.18520.74070.00120.18010.4596-0.02050.571222.687885.6202113.5155
250.702-0.5534-0.3080.90.78760.7014-0.0197-0.10140.1153-0.72420.06250.49880.1513-0.1892-0.00020.93480.0899-0.03280.5262-0.01150.5919-4.432165.7079118.0935
260.2167-0.0452-0.21340.2342-0.15350.3328-0.21030.1991-0.15590.7259-0.1197-0.0447-1.3253-0.7239-0.04281.00090.2222-0.35260.638-0.07050.6493-10.424567.4738110.2037
270.54510.0611-0.34820.5571-0.07510.44330.1913-0.2770.4743-0.315-0.17021.0683-0.4673-0.1740.00620.77240.109-0.31480.5889-0.07150.6803-10.728668.1669119.5528
280.3466-0.2103-0.19360.12580.14840.44230.3143-1.05040.23320.0716-0.59140.79650.136-0.1615-0.00080.48340.0568-0.01080.6371-0.04210.7093-6.904169.9235129.3284
290.50690.42380.03311.08130.53020.5782-0.2002-0.1854-0.0096-0.17640.03110.1006-0.2685-0.1747-0.00030.5950.1229-0.04130.45350.0140.5131-5.716972.711131.6502
300.70290.25020.00840.27420.27121.31870.0518-0.2143-0.3363-0.2706-0.10360.5167-0.0643-0.09180.00340.71990.0155-0.03360.4302-0.03240.43684.756460.8854119.2892
312.44990.8563-0.4231.06770.00380.6951-0.23360.0737-0.8353-0.52280.0218-0.4185-0.0854-0.0426-0.13570.95260.08910.03090.3373-0.1070.23928.706257.3075110.6353
320.4334-0.4632-0.17440.38180.13340.9978-0.19530.464-0.5166-0.0892-0.09650.5807-0.2859-0.0832-0.00220.7212-0.0135-0.0580.5142-0.00880.49782.122345.0572111.7037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 24 THROUGH 39 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 40 THROUGH 55 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 56 THROUGH 94 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 95 THROUGH 114 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 115 THROUGH 140 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 141 THROUGH 186 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 187 THROUGH 209 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 210 THROUGH 225 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 226 THROUGH 240 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 24 THROUGH 39 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 40 THROUGH 55 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 56 THROUGH 94 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 95 THROUGH 114 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 115 THROUGH 140 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 141 THROUGH 169 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 170 THROUGH 215 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 216 THROUGH 240 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 24 THROUGH 55 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 56 THROUGH 94 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 95 THROUGH 114 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 115 THROUGH 127 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 128 THROUGH 186 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 187 THROUGH 215 )
24X-RAY DIFFRACTION24CHAIN 'C' AND (RESID 216 THROUGH 240 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 24 THROUGH 39 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 40 THROUGH 55 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 56 THROUGH 81 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 82 THROUGH 94 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 95 THROUGH 140 )
30X-RAY DIFFRACTION30CHAIN 'D' AND (RESID 141 THROUGH 169 )
31X-RAY DIFFRACTION31CHAIN 'D' AND (RESID 170 THROUGH 215 )
32X-RAY DIFFRACTION32CHAIN 'D' AND (RESID 216 THROUGH 240 )

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