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- PDB-7rgb: O2-, PLP-dependent desaturase Plu4 product-bound enzyme -

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Basic information

Entry
Database: PDB / ID: 7rgb
TitleO2-, PLP-dependent desaturase Plu4 product-bound 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 / Chem-4VI / Aminotransferase class I/classII domain-containing protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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
DepositionJul 14, 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
C: Aminotran_1_2 domain-containing protein
D: Aminotran_1_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,89514
Polymers179,4694
Non-polymers1,42610
Water3,315184
1
A: Aminotran_1_2 domain-containing protein
B: Aminotran_1_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3856
Polymers89,7352
Non-polymers6514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-14 kcal/mol
Surface area25210 Å2
MethodPISA
2
C: Aminotran_1_2 domain-containing protein
D: Aminotran_1_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5098
Polymers89,7352
Non-polymers7756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-15 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.372, 72.186, 139.626
Angle α, β, γ (deg.)90.000, 98.440, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4
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.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-4VI / (2Z,4E)-5-carbamimidamido-2-iminopent-4-enoic acid


Mass: 170.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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 and 3 mM L-arginine for 16 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: 2.5→39.74 Å / Num. obs: 51795 / % possible obs: 99.1 % / Redundancy: 13.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.073 / Rrim(I) all: 0.27 / Net I/σ(I): 7.3 / Num. measured all: 706448 / Scaling rejects: 1599
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
2.5-2.5813.15.5085843144440.4861.5765.7411.598
10.31-39.7413.90.074110997960.9980.020.07617.398.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C3D

6c3d


Resolution: 2.5→37.772 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 46.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 2577 5.05 %
Rwork0.2342 48495 -
obs0.236 51072 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.38 Å2 / Biso mean: 67.3216 Å2 / Biso min: 26.61 Å2
Refinement stepCycle: final / Resolution: 2.5→37.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11494 0 96 184 11774
Biso mean--78.01 54.77 -
Num. residues----1486
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.54820.45251250.4094258693
2.5482-2.60020.44241520.3613265498
2.6002-2.65670.3491450.351268998
2.6567-2.71850.38691410.3376268298
2.7185-2.78650.3521500.3375263597
2.7865-2.86180.36941270.3289270897
2.8618-2.94590.38691380.3045271999
2.9459-3.0410.35831440.28782756100
3.041-3.14960.3171400.2742737100
3.1496-3.27570.30281680.26492727100
3.2757-3.42470.2821330.25662739100
3.4247-3.60510.28911410.2444274098
3.6051-3.83070.26281330.2222271098
3.8307-4.12620.21831250.196266997
4.1262-4.54080.22941630.1901274399
4.5408-5.19640.2511610.1771275499
5.1964-6.54140.20461450.2032278699
6.5414-37.7720.20481460.1761246186
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)
12.48851.021-0.14812.089-1.69881.54720.17040.02150.12440.4189-0.22570.0842-0.87480.2463-0.01460.75490.0027-0.0190.5864-0.04890.489431.901140.349649.4335
23.4730.0243-0.06862.355-1.03493.55160.1547-0.4649-0.12750.0201-0.08560.71520.0799-0.2334-0.02810.536-0.09120.12240.49860.01460.674217.506923.123355.9668
32.3338-0.3480.91552.5343-0.52621.90840.1089-0.37970.16690.2976-0.14660.6467-0.5062-0.18020.01810.7222-0.05670.18330.4256-0.11510.429321.743234.927956.823
45.96810.07290.1172.508-2.4925.68650.2210.3242-0.3586-0.69460.10040.81020.2976-0.3992-0.27120.81970.0457-0.1320.3585-0.02730.800812.86931.981231.2819
52.06082.4872-1.15026.3483-3.16444.46860.32720.6378-0.43120.0027-0.25590.75470.0133-0.3519-0.10590.5750.1986-0.06550.2714-0.16170.567117.796731.839832.7866
62.5920.41350.80342.55140.21580.29070.10340.02070.0730.0864-0.228-0.3172-0.0570.49760.21980.7792-0.04550.01080.7650.07390.457247.290135.381352.7876
72.8698-1.3539-0.50215.0254-0.88751.3950.2112-0.19750.1477-0.1164-0.32220.0048-0.07040.79340.17440.47310.082-0.05370.687-0.02030.26544.888613.8350.9221
82.8538-0.4648-1.24224.45910.71383.2050.44630.0063-0.133-0.8957-0.8018-0.72050.18721.20220.25380.72780.36150.15431.09740.22560.505855.85810.596349.2693
92.6117-0.34860.85212.1335-0.19252.34280.21530.3398-0.0197-0.1215-0.4708-0.34210.12260.73630.25260.65160.01690.09230.87780.07650.40149.385726.549847.5882
103.60731.28962.60743.41783.08513.59080.3603-0.28340.32090.6788-0.2486-0.37670.26130.6671-0.06320.8465-0.1588-0.01420.95590.13350.426556.511323.330672.5615
112.450.15670.59663.48923.5373.83590.43070.101-0.14310.5582-0.4042-0.25831.2902-0.8136-0.01740.6267-0.0769-0.03540.40590.00820.47020.7586-6.744434.4895
122.0339-0.55950.72571.41371.64282.7943-0.3296-0.12670.637-0.15380.12010.0331-0.7534-0.12680.23920.8116-0.01550.04650.38150.11960.6396-6.27169.743612.2192
133.1088-0.63560.7592.3384-0.07143.07120.17450.2314-0.3648-0.4091-0.0906-0.009-0.32840.4976-0.07060.5149-0.04430.08030.2827-0.02130.34231.6538-8.01576.8814
143.28270.99650.37510.604-0.29323.07230.26190.2057-0.52070.28990.0373-0.7710.39920.5439-0.28760.44570.1112-0.01710.3994-0.09230.67314.4605-15.229515.9313
151.6706-0.21390.35652.24090.48042.20010.04760.24490.0933-0.2068-0.0996-0.4459-0.27170.06950.07090.4867-0.10550.08380.37720.01560.58765.1805-3.39419.3264
163.3462-0.61324.20324.16182.43819.2076-0.77670.29570.539-1.08160.101-0.9053-1.04890.32780.52390.3536-0.14590.07130.32530.01660.771111.808111.000128.1497
174.2196-1.17260.77090.3701-0.11142.0666-0.2003-0.1346-0.01630.24210.1331-0.50390.61050.2604-0.03920.8512-0.1227-0.19840.4616-0.1160.748315.0428-4.131137.7806
182.8778-1.94321.44815.38490.17945.5227-0.2053-0.10990.26641.8131-0.0024-0.6452-0.11910.05680.14950.5275-0.0137-0.16930.4682-0.03710.539910.1586-4.266136.2468
191.3274-0.19981.4373.4221-1.44172.01670.07260.37160.28890.0834-0.5979-0.1866-0.3243-0.13910.35560.42040.1822-0.04920.9048-0.06440.4685-20.8469-4.40383.5063
204.6777-0.92580.97441.5571-1.56321.981-0.4296-0.33320.71730.831-0.2339-0.2826-0.6262-0.33260.39620.43880.1380.05990.6572-0.15220.568-17.92662.717428.2689
213.0171.2907-0.38272.3352-0.54450.72620.2892-0.687-0.15190.02970.17840.05250.6227-0.565-0.38840.6533-0.20890.12510.6923-0.0120.3785-15.7068-16.36325.4062
222.34980.4784-0.16260.8091-0.20791.43130.3055-0.1738-0.69430.3288-0.31310.41861.0566-0.75410.05410.7491-0.37140.17590.7248-0.06290.6383-24.0142-26.161217.0091
233.4550.12130.19682.91831.03752.22680.1309-0.44390.07940.573-0.30470.28720.1343-0.93170.13020.5177-0.10570.09970.5712-0.06990.3597-17.7165-11.09824.5628
240.5641-0.625-1.23362.57170.05093.68060.0163-0.6583-0.05250.0070.1840.89160.1823-0.6464-0.11110.16750.06480.09760.94850.00450.6513-36.6796-7.57576.6171
257.23391.03510.8775.5367-1.6293.2150.09371.0006-0.235-1.24650.01050.62110.3308-0.241-0.08240.73040.0843-0.16970.9336-0.21040.5412-27.7349-14.2737-8.4223
265.7275-2.66890.969.4708-2.91075.9025-0.19690.4775-0.6044-0.8671-0.180.37130.3872-1.39290.37330.5408-0.11150.09190.7154-0.18980.5002-24.3148-17.0235-0.5875
276.07671.85384.47795.04910.41337.859-0.07510.28150.8405-0.6971-0.22460.7742-1.1543-0.54790.53920.54470.2372-0.20190.9114-0.0360.5738-31.6911-2.1076-6.8673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 70 )A6 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 166 )A71 - 166
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 290 )A167 - 290
4X-RAY DIFFRACTION4chain 'A' and (resid 291 through 331 )A291 - 331
5X-RAY DIFFRACTION5chain 'A' and (resid 332 through 379 )A332 - 379
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 69 )B6 - 69
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 136 )B70 - 136
8X-RAY DIFFRACTION8chain 'B' and (resid 137 through 199 )B137 - 199
9X-RAY DIFFRACTION9chain 'B' and (resid 200 through 290 )B200 - 290
10X-RAY DIFFRACTION10chain 'B' and (resid 291 through 380 )B291 - 380
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 28 )C6 - 28
12X-RAY DIFFRACTION12chain 'C' and (resid 29 through 70 )C29 - 70
13X-RAY DIFFRACTION13chain 'C' and (resid 71 through 100 )C71 - 100
14X-RAY DIFFRACTION14chain 'C' and (resid 101 through 166 )C101 - 166
15X-RAY DIFFRACTION15chain 'C' and (resid 167 through 270 )C167 - 270
16X-RAY DIFFRACTION16chain 'C' and (resid 271 through 290 )C271 - 290
17X-RAY DIFFRACTION17chain 'C' and (resid 291 through 331 )C291 - 331
18X-RAY DIFFRACTION18chain 'C' and (resid 332 through 379 )C332 - 379
19X-RAY DIFFRACTION19chain 'D' and (resid 6 through 36 )D6 - 36
20X-RAY DIFFRACTION20chain 'D' and (resid 37 through 69 )D37 - 69
21X-RAY DIFFRACTION21chain 'D' and (resid 70 through 100 )D70 - 100
22X-RAY DIFFRACTION22chain 'D' and (resid 101 through 199 )D101 - 199
23X-RAY DIFFRACTION23chain 'D' and (resid 200 through 270 )D200 - 270
24X-RAY DIFFRACTION24chain 'D' and (resid 271 through 308 )D271 - 308
25X-RAY DIFFRACTION25chain 'D' and (resid 309 through 331 )D309 - 331
26X-RAY DIFFRACTION26chain 'D' and (resid 332 through 360 )D332 - 360
27X-RAY DIFFRACTION27chain 'D' and (resid 361 through 380 )D361 - 380

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