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- PDB-6o55: Crystal Structure of N5-carboxyaminoimidazole ribonucleotide muta... -

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Basic information

Entry
Database: PDB / ID: 6o55
TitleCrystal Structure of N5-carboxyaminoimidazole ribonucleotide mutase (PurE) from Legionella pneumophila
ComponentsN5-carboxyaminoimidazole ribonucleotide mutase
KeywordsISOMERASE / SSGCID / mutase / carboxylase / phosphorobosylaminoimidazole carboxylase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process / lyase activity
Similarity search - Function
: / Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of N5-carboxyaminoimidazole ribonucleotide mutase (PurE) from Legionella pneumophila
Authors: Bolejack, M.J. / Edwards, T.E. / Lorimer, D.D. / Horanyi, P.S.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
C: N5-carboxyaminoimidazole ribonucleotide mutase
D: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,01815
Polymers74,3104
Non-polymers70811
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-65 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.280, 88.560, 52.510
Angle α, β, γ (deg.)90.000, 111.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-394-

HOH

21A-412-

HOH

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Components

#1: Protein
N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase


Mass: 18577.426 Da / Num. of mol.: 4 / Fragment: LepnA.01377.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: purE, lpg0218 / Plasmid: LepnA.01377.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5ZYZ3, 5-(carboxyamino)imidazole ribonucleotide mutase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: LepnA.01377.a.B1.PS38521 at 19 mg/ml was mixed 1:1 with MCSG-1(a3): 0.2 M sodium chloride, 0.1 M sodium phosphate/potassium phosphate pH 6.2, 10% (w/v) PEG 8000. Tray: 305565a3, puck: ywm0-1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 7, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→48.336 Å / Num. obs: 63895 / % possible obs: 99.5 % / Redundancy: 3.689 % / Biso Wilson estimate: 27.015 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.06 / Χ2: 1.06 / Net I/σ(I): 16.68 / Num. measured all: 235703 / Scaling rejects: 53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.743.6050.6032.447480.8610.7199.8
1.74-1.793.6850.4563.1545470.9220.53499.8
1.79-1.843.6830.3374.1244570.9550.39499.6
1.84-1.93.6920.2515.4343790.9750.29599.3
1.9-1.963.6870.1996.9541810.980.23399.5
1.96-2.033.7070.1478.8940270.9880.17299.4
2.03-2.113.7110.11611.0739620.9910.13699.3
2.11-2.193.7140.09512.8937700.9940.11199.4
2.19-2.293.6250.08814.8436040.9940.10499.1
2.29-2.43.7070.06717.8134800.9960.07899.4
2.4-2.533.7270.05620.8432850.9970.06599.7
2.53-2.693.7270.04823.4931330.9970.05699.8
2.69-2.873.7170.04426.6229440.9970.05299.5
2.87-3.13.7120.03730.3927370.9980.04399.8
3.1-3.43.70.03135.7925430.9980.03699.3
3.4-3.83.6610.02937.5722840.9980.03499.5
3.8-4.393.7130.02540.920210.9990.02999.5
4.39-5.383.7180.02243.0817060.9990.02699.5
5.38-7.63.70.02240.913420.9990.02699.3
7.6-48.3363.5330.0245.227450.9990.02498.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OOW

3oow


Resolution: 1.7→48.336 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.84
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 2106 3.3 %0
Rwork0.1478 ---
obs0.1489 63827 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.41 Å2 / Biso mean: 25.415 Å2 / Biso min: 9.43 Å2
Refinement stepCycle: final / Resolution: 1.7→48.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 41 605 5408
Biso mean--49.01 34.78 -
Num. residues----646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6999-1.73950.28981260.250441404266100
1.7395-1.7830.31261190.228840934212100
1.783-1.83120.25071580.208440674225100
1.8312-1.88510.19061360.18594114425099
1.8851-1.94590.23761160.19564129424599
1.9459-2.01550.21091430.16834073421699
2.0155-2.09620.19571830.16344060424399
2.0962-2.19160.21821440.15164081422599
2.1916-2.30710.22531280.1614092422099
2.3071-2.45170.19611600.140341174277100
2.4517-2.6410.19671360.142441294265100
2.641-2.90670.16721600.147641064266100
2.9067-3.32720.1591390.137141344273100
3.3272-4.19160.14721210.120941634284100
4.1916-48.35590.13391370.122642234360100
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)
11.35581.3768-0.12466.38931.6871.02140.2848-0.6262-0.66440.1384-0.1834-0.21040.1713-0.2855-0.05730.3041-0.062-0.08010.20030.1370.3535.3527-29.847514.0435
24.56722.8576-0.27842.77840.11260.16820.1769-0.473-0.28160.10720.0216-0.06540.1011-0.2175-0.14330.293-0.0476-0.04410.29280.12140.1858-0.4191-22.559118.0625
36.40653.62960.65982.3090.43560.10560.218-0.4494-0.5630.2343-0.0659-0.0206-0.0111-0.1749-0.09850.304-0.0356-0.06520.21890.11030.29257.505-26.661415.4276
45.12765.44831.31146.27592.11793.18560.2002-0.129-0.85650.1194-0.1027-0.30260.10560.1236-0.11030.21410.016-0.07170.15490.0510.288618.5816-28.34710.2789
52.6362-0.0209-1.17545.6562-0.01612.76420.1486-0.0326-0.48960.1064-0.1356-0.50620.46230.56830.02390.3704-0.0053-0.17620.08440.08040.74359.7669-37.21528.0089
63.0194-0.3645-0.12340.0873-0.07131.46310.1393-0.0302-0.3470.1004-0.0431-0.11190.026-0.023-0.09370.2095-0.0116-0.04190.10880.02520.20298.8401-22.71575.9545
75.2079-0.23913.20761.81752.77796.76740.2858-1.3960.67050.8625-0.61950.93830.1727-0.90080.27260.2931-0.07280.09420.3293-0.09640.26022.1144-5.995212.0641
82.01440.24080.70221.484-0.010.82430.1973-0.1894-0.45380.0565-0.02250.03010.125-0.0386-0.12530.1979-0.004-0.04210.10870.04050.19910.8029-22.22963.6687
97.2254-6.3097-0.72718.59580.64940.96150.0267-0.2003-0.78460.2595-0.00170.34540.1141-0.182-0.02240.2532-0.077-0.04580.22680.11850.3287-19.1048-28.72399.4258
103.4786-0.1167-3.29676.23110.71033.161-0.3385-0.52550.15490.58160.2515-0.40880.08520.14810.08580.20390.0002-0.03080.1625-0.03260.122625.66388.752719.4325
116.1248-4.621.88336.5643-1.88562.129-0.2997-0.4539-0.04950.66790.19980.1629-0.0163-0.24250.09940.252-0.00980.02290.2251-0.02660.08517.1454.294123.0887
127.2162-7.68135.32069.3032-5.93364.7948-0.1043-0.07720.27420.2421-0.0892-0.2533-0.0455-0.02440.250.1423-0.0106-0.00230.1613-0.04260.116721.961611.860919.0624
134.6136-6.41883.77799.0032-5.12915.955-0.0709-0.2460.50990.3269-0.0581-0.2508-0.2915-0.07780.19380.1538-0.0153-0.00030.1351-0.03830.17225.972920.19512.212
146.3638-1.5014.68712.3972-0.93914.2025-0.02470.02720.07240.00730.0099-0.0537-0.07360.07630.00940.1411-0.00030.03170.1254-0.01160.120824.652610.38612.5034
151.3056-0.12120.2582.1807-0.46480.9826-0.04690.04560.14560.0341-0.026-0.2113-0.0313-0.0550.0640.13680.01180.00220.1381-0.01670.122622.631810.12368.1647
169.0325-3.64812.62143.1783-1.45293.4962-0.4638-0.9287-0.58760.76930.40010.89830.2005-0.49590.0350.22780.02630.07580.30060.05780.29092.37165.20711.9103
171.8216-0.33830.47961.212-0.22860.455-0.0094-0.0640.06140.07750.0286-0.08370.0048-0.0363-0.01620.15250.00420.01690.1121-0.01070.084920.49171.65619.0468
188.17825.5856-1.9995.8522-2.04212.49180.1974-0.6196-0.26610.314-0.1724-0.35020.12620.10040.01460.2240.0223-0.05970.17260.03610.155927.5931-13.377220.4499
192.77262.7255-1.72682.751-1.60032.0670.1239-1.9056-0.66060.3595-0.20280.1095-0.1593-0.46490.2090.3655-0.0443-0.05350.45850.07850.318211.1892-24.047924.5174
200.79140.30760.00535.2872-1.03684.20790.0079-0.40140.7510.3093-0.04550.1398-0.16720.11860.05160.18170.03520.00930.1997-0.11320.3673-11.570430.04939.6135
213.49092.64061.77362.78311.03631.046-0.0622-0.73790.54980.0465-0.0390.2345-0.00090.00050.07310.21640.02590.04040.2708-0.1150.2176-8.941222.415115.7971
223.10411.11910.86940.57260.78391.1908-0.1547-0.20670.48480.1440.0551-0.0717-0.0499-0.12380.13430.18610.03250.01420.1504-0.07620.2942-17.21627.18665.0447
232.6814-3.20390.19034.01130.33482.06940.111-0.03430.7093-0.1385-0.18210.5083-0.0327-0.0287-0.04440.17390.0032-0.0210.1143-0.03610.3886-11.097330.5713.2395
242.5342-0.10691.18550.2309-0.64642.8675-0.0684-0.05810.31460.06830.00110.16130.0166-0.07490.07090.14510.01310.01890.114-0.03550.2217-10.968922.0176-0.7293
253.69421.1684-1.29898.4721-0.55444.03050.5264-1.1054-0.39411.4459-0.6621-0.1790.5549-0.30820.1050.3843-0.1125-0.0090.2880.04720.1958-7.97845.3229.0429
262.20040.12450.43941.4680.4470.783-0.0615-0.14520.46360.0493-0.00090.0157-0.0192-0.06050.02570.1210.01250.01410.0974-0.02830.1957-2.575221.98832.7314
277.6906-5.96864.15114.7558-3.17082.8575-0.506-0.26930.87680.65870.0716-0.1693-0.4375-0.03650.38840.21940.0019-0.04020.1838-0.10110.37219.576331.852715.4414
287.82412.6150.45294.61235.44918.92730.1876-0.4581-0.2671.3350.3038-0.44030.24770.1845-0.41840.2812-0.008-0.04290.303-0.08890.180218.981717.057326.1916
290.56570.9941.08025.4675-1.30484.61060.0753-0.3527-0.01780.06750.07950.59410.0466-0.3538-0.12720.1992-0.03560.04680.24140.02450.1813-33.2509-8.78654.0263
304.546-4.51751.62816.667-1.28681.2734-0.2317-0.4516-0.25230.71990.220.2788-0.1363-0.0269-0.01770.2646-0.03680.07290.26820.03760.1387-26.5881-4.498710.9661
317.4397-5.81740.74924.5071-0.64620.39510.1122-0.509-0.3258-0.00270.09890.27920.0303-0.0647-0.18960.1852-0.04670.02960.23110.05440.2385-29.1009-11.55925.3754
327.573-6.51324.01565.7845-4.18844.51040.3498-0.0959-0.7337-0.5135-0.08750.61450.4918-0.0928-0.30570.2526-0.0443-0.00610.17850.03390.2533-28.5103-20.4127-3.0234
338.5532-1.83494.59281.7659-0.50583.1012-0.0347-0.07370.0010.03190.05160.2260.0889-0.1775-0.06020.1562-0.03740.01040.13020.03760.1295-27.5366-10.6337-1.8899
342.7806-0.11261.61950.68590.62822.28990.1304-0.0894-0.18840.0893-0.0490.05670.1596-0.0637-0.0760.161-0.02480.00280.14290.02210.1277-23.6-10.4051-4.5472
352.9814-0.14153.61363.4627-3.31937.3019-0.7816-0.91250.71091.3750.443-0.4479-0.819-0.49780.18420.41730.0764-0.06150.2772-0.03770.1906-8.235-5.69588.9981
362.2935-0.46120.06571.32620.08540.46240.0219-0.1088-0.06570.05740.01490.1370.0559-0.0373-0.03570.1424-0.01720.01510.11930.00920.0981-22.2241-1.9199-2.6757
376.28915.50915.70314.93875.11995.4220.0151-0.49950.11620.054-0.20830.5177-0.0045-0.53630.29880.16910.01550.07420.2244-0.010.2545-34.233113.05873.5154
381.0652.7074-0.47547.5214-0.4492.25130.1735-1.52890.56830.6325-0.0196-0.2626-0.2011-0.1588-0.14530.26420.02610.03190.4105-0.11720.2148-21.926424.792615.4654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 12 )A2 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 28 )A13 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 43 )A29 - 43
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 54 )A44 - 54
5X-RAY DIFFRACTION5chain 'A' and (resid 55 through 60 )A55 - 60
6X-RAY DIFFRACTION6chain 'A' and (resid 61 through 89 )A61 - 89
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 96 )A90 - 96
8X-RAY DIFFRACTION8chain 'A' and (resid 97 through 137 )A97 - 137
9X-RAY DIFFRACTION9chain 'A' and (resid 138 through 162 )A138 - 162
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 12 )B2 - 12
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 28 )B13 - 28
12X-RAY DIFFRACTION12chain 'B' and (resid 29 through 43 )B29 - 43
13X-RAY DIFFRACTION13chain 'B' and (resid 44 through 54 )B44 - 54
14X-RAY DIFFRACTION14chain 'B' and (resid 55 through 71 )B55 - 71
15X-RAY DIFFRACTION15chain 'B' and (resid 72 through 89 )B72 - 89
16X-RAY DIFFRACTION16chain 'B' and (resid 90 through 96 )B90 - 96
17X-RAY DIFFRACTION17chain 'B' and (resid 97 through 137 )B97 - 137
18X-RAY DIFFRACTION18chain 'B' and (resid 138 through 156 )B138 - 156
19X-RAY DIFFRACTION19chain 'B' and (resid 157 through 162 )B157 - 162
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 12 )C2 - 12
21X-RAY DIFFRACTION21chain 'C' and (resid 13 through 28 )C13 - 28
22X-RAY DIFFRACTION22chain 'C' and (resid 29 through 54 )C29 - 54
23X-RAY DIFFRACTION23chain 'C' and (resid 55 through 67 )C55 - 67
24X-RAY DIFFRACTION24chain 'C' and (resid 68 through 89 )C68 - 89
25X-RAY DIFFRACTION25chain 'C' and (resid 90 through 96 )C90 - 96
26X-RAY DIFFRACTION26chain 'C' and (resid 97 through 137 )C97 - 137
27X-RAY DIFFRACTION27chain 'C' and (resid 138 through 156 )C138 - 156
28X-RAY DIFFRACTION28chain 'C' and (resid 157 through 162 )C157 - 162
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 12 )D1 - 12
30X-RAY DIFFRACTION30chain 'D' and (resid 13 through 28 )D13 - 28
31X-RAY DIFFRACTION31chain 'D' and (resid 29 through 43 )D29 - 43
32X-RAY DIFFRACTION32chain 'D' and (resid 44 through 54 )D44 - 54
33X-RAY DIFFRACTION33chain 'D' and (resid 55 through 71 )D55 - 71
34X-RAY DIFFRACTION34chain 'D' and (resid 72 through 89 )D72 - 89
35X-RAY DIFFRACTION35chain 'D' and (resid 90 through 96 )D90 - 96
36X-RAY DIFFRACTION36chain 'D' and (resid 97 through 137 )D97 - 137
37X-RAY DIFFRACTION37chain 'D' and (resid 138 through 156 )D138 - 156
38X-RAY DIFFRACTION38chain 'D' and (resid 157 through 163 )D157 - 163

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