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- PDB-7n79: O2-, PLP-dependent desaturase Plu4 holo-enzyme -

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Basic information

Entry
Database: PDB / ID: 7n79
TitleO2-, PLP-dependent desaturase Plu4 holo-enzyme
ComponentsAminotran_1_2 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / arginine desaturase / oxygen- and PLP-dependent oxidase / Fold Type I / biosynthesis
Function / homologybiosynthetic process / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / ACETATE ION / Aminotransferase class I/classII domain-containing protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHoffarth, E.R. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-03778 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases.
Authors: Hoffarth, E.R. / Caddell Haatveit, K. / Kuatsjah, E. / MacNeil, G.A. / Saroya, S. / Walsby, C.J. / Eltis, L.D. / Houk, K.N. / Garcia-Borras, M. / Ryan, K.S.
History
DepositionJun 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotran_1_2 domain-containing protein
B: Aminotran_1_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,51610
Polymers89,7352
Non-polymers7828
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-5 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.022, 72.195, 76.271
Angle α, β, γ (deg.)90.000, 112.090, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Aminotran_1_2 domain-containing protein / Oxygen- / PLP-dependent L-arginine desaturase


Mass: 44867.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas luteoviolacea (bacteria)
Gene: JF50_03865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C1MLE8
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.33 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris:HCl; 27% PEG 3350; 0.2 M ammonium acetate; microseeded from crystals grown at pH 6.0; soaked with 2 mM PLP for 2 h
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.98→37.75 Å / Num. obs: 52155 / % possible obs: 98.6 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 15.2
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
1.98-2.036.62.0122314735100.5140.8382.1851.494.2
9.06-37.757.20.05142095880.9980.020.0554899

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C3D

6c3d


Resolution: 1.98→37.75 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 2642 5.07 %
Rwork0.166 49478 -
obs0.1684 52120 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.3 Å2 / Biso mean: 51.4718 Å2 / Biso min: 25.75 Å2
Refinement stepCycle: final / Resolution: 1.98→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 52 330 6386
Biso mean--79.53 51.69 -
Num. residues----756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.98-2.01290.32351130.2934247192
2.0129-2.05160.31821350.25562590100
2.0516-2.09350.32231600.2471260199
2.0935-2.1390.29321580.2276259799
2.139-2.18870.2891460.2223260499
2.1887-2.24350.26751420.2136260599
2.2435-2.30410.25261470.2083245495
2.3041-2.37190.25221550.194259298
2.3719-2.44850.24591050.18512637100
2.4485-2.53590.23641370.18342639100
2.5359-2.63750.25941490.19032643100
2.6375-2.75750.26351320.1871261999
2.7575-2.90280.26931410.1864260999
2.9028-3.08460.24721300.1812256397
3.0846-3.32260.24281460.1765261699
3.3226-3.65670.19141550.1603262899
3.6567-4.18530.19331250.1353266699
4.1853-5.27070.13561190.1277265599
5.2707-37.750.18651470.1488268999
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)
11.6546-1.2286-0.42795.2425-0.21771.89620.035-0.17390.058-0.2568-0.04880.3439-0.121-0.47570.1430.3119-0.04010.06520.6443-0.09610.4418.066230.770355.0953
22.52780.2491-0.10343.5482-0.15330.81230.224-0.79060.3720.5859-0.1415-0.3839-0.19130.1249-0.32320.3971-0.0574-0.06950.4801-0.10910.366742.795138.29563.054
32.49670.07970.21063.063-0.13514.08910.0924-0.7803-0.51670.4411-0.1325-0.5797-0.14940.1983-0.32060.3117-0.0591-0.07620.44370.13790.337841.129619.248358.9934
43.73880.5082-0.09494.56020.00072.2052-0.0273-0.474-0.4838-0.0065-0.0955-0.10260.4785-0.2208-0.13790.3295-0.0895-0.00560.31660.08510.341729.57129.655153.1096
50.7065-1.0417-1.1441.80621.26572.52890.1615-1.3139-0.75490.724-0.15930.18360.4866-0.2588-0.42860.6222-0.2659-0.01160.83770.23140.60825.43973.317367.6553
62.43960.04770.46580.6738-1.04791.79410.2635-1.0594-0.57370.58-0.4525-0.19980.4749-0.3239-0.57290.5031-0.1797-0.07290.70680.28270.469128.13310.082165.3009
71.236-0.1811.06823.0411-2.24672.59710.332-1.6242-0.65890.8792-0.527-0.48790.3264-0.3112-0.93780.6738-0.3193-0.18260.87070.44690.4933.550912.723770.5158
82.1090.5113-0.46764.4485-0.23282.32070.1688-0.7524-0.30590.4771-0.3922-0.41540.15780.0814-0.51140.3543-0.1083-0.0690.52480.12640.310737.551821.341763.3234
91.61620.495-0.29232.4660.12332.06670.1683-0.66220.0420.2705-0.2337-0.1204-0.1809-0.0463-0.34390.2771-0.0593-0.06610.40740.00160.248640.111729.819760.4063
102.52620.0231-0.47543.65570.58051.86420.1969-0.59-0.05330.4058-0.28820.48690.0766-0.5761-0.10630.382-0.12490.07210.7476-0.06750.39511.32222.615662.8513
118.44163.1131.79166.93061.14692.37020.1172-0.8910.01920.089-0.32740.6605-0.2936-0.73120.15520.44420.06310.09070.7966-0.1370.58073.257433.024761.7445
122.9639-0.26860.4665.0120.30182.6672-0.0288-0.2611-0.1419-0.08970.1546-0.10460.03270.2314-0.06380.2698-0.03680.06220.32590.05390.407753.299633.618846.7141
131.8414-0.141-0.35860.7570.67361.44590.0022-0.05940.5809-0.1061-0.08660.224-0.4236-0.36080.00910.38990.0921-0.03870.3443-0.02810.494428.69344.810546.2207
142.95250.2279-0.76385.49140.51622.3548-0.05880.46780.3327-0.2962-0.00050.4724-0.0793-0.34960.13120.24970.0087-0.04780.30110.00780.267730.408928.43835.8961
151.79960.4722-0.91330.6477-0.70783.2138-0.13820.4468-0.5563-0.62930.0577-0.32040.3402-0.0163-0.17290.4713-0.01320.09420.2315-0.07030.399442.107116.711234.5842
162.46230.17242.01555.07420.07864.58430.17081.2322-0.3097-0.77180.0378-0.06390.14520.1931-0.60330.74980.06650.18660.62-0.14670.523445.521820.623918.8384
173.83660.42620.19172.29410.13052.55610.0250.7271-0.0202-0.5172-0.0359-0.16810.0262-0.2433-0.18940.51650.04110.05870.44770.00410.321539.959528.58724.2851
182.81181.01180.08671.58261.01752.74590.1180.32690.2846-0.3256-0.07620.11290.0011-0.4084-0.0280.39790.0674-0.04550.30880.04250.31734.802132.765234.7241
192.7860.7024-0.22654.75990.49332.32650.01410.07460.4851-0.0681-0.0910.4733-0.1077-0.27830.01640.21350.0683-0.06150.2804-0.00790.327829.262533.950142.2482
205.6971-1.96880.42294.4070.381.265-0.30090.32491.6169-0.46670.1794-0.614-0.50320.08760.12740.5458-0.01810.05570.26850.1010.660154.61846.340734.8598
214.05530.06370.21832.49160.12472.05980.06880.3815-0.2482-0.3425-0.0597-0.6524-0.14660.31360.03710.3707-0.01510.15140.33320.05010.738463.421631.821934.3903
222.24171.37090.57115.3162.45772.69540.16960.0571-0.1032-0.2614-0.0011-0.80640.01930.2336-0.23270.33250.0220.12560.24360.05720.488657.993226.351937.0907
234.5699-3.0063-0.33616.4421.54813.01260.161-0.16480.0444-0.05970.023-0.7954-0.04820.5689-0.0770.3958-0.07450.0080.40940.01260.659367.934539.873643.5659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 36 )A5 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 70 )A37 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 100 )A71 - 100
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 125 )A101 - 125
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 144 )A126 - 144
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 166 )A145 - 166
7X-RAY DIFFRACTION7chain 'A' and (resid 167 through 199 )A167 - 199
8X-RAY DIFFRACTION8chain 'A' and (resid 200 through 237 )A200 - 237
9X-RAY DIFFRACTION9chain 'A' and (resid 238 through 275 )A238 - 275
10X-RAY DIFFRACTION10chain 'A' and (resid 276 through 360 )A276 - 360
11X-RAY DIFFRACTION11chain 'A' and (resid 361 through 381 )A361 - 381
12X-RAY DIFFRACTION12chain 'B' and (resid 5 through 36 )B5 - 36
13X-RAY DIFFRACTION13chain 'B' and (resid 37 through 69 )B37 - 69
14X-RAY DIFFRACTION14chain 'B' and (resid 70 through 100 )B70 - 100
15X-RAY DIFFRACTION15chain 'B' and (resid 101 through 125 )B101 - 125
16X-RAY DIFFRACTION16chain 'B' and (resid 126 through 146 )B126 - 146
17X-RAY DIFFRACTION17chain 'B' and (resid 147 through 199 )B147 - 199
18X-RAY DIFFRACTION18chain 'B' and (resid 200 through 234 )B200 - 234
19X-RAY DIFFRACTION19chain 'B' and (resid 235 through 270 )B235 - 270
20X-RAY DIFFRACTION20chain 'B' and (resid 271 through 291 )B271 - 291
21X-RAY DIFFRACTION21chain 'B' and (resid 292 through 331 )B292 - 331
22X-RAY DIFFRACTION22chain 'B' and (resid 332 through 360 )B332 - 360
23X-RAY DIFFRACTION23chain 'B' and (resid 361 through 381 )B361 - 381

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