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- PDB-4nq3: Crystal structure of cyanuic acid hydrolase from A. caulinodans -

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Basic information

Entry
Database: PDB / ID: 4nq3
TitleCrystal structure of cyanuic acid hydrolase from A. caulinodans
ComponentsCyanuric acid amidohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


cyanuric acid amidohydrolase / cyanuric acid amidohydrolase activity / atrazine catabolic process / metal ion binding
Similarity search - Function
Cyanuric acid hydrolase/Barbiturase, RU B / Cyanuric acid hydrolase/Barbituras, RU C / Cyanuric acid hydrolase/Barbiturase, RU A / Cyanuric acid hydrolase/Barbiturase / Cyanuric acid hydrolase/Barbiturase, repeating unit B / Cyanuric acid hydrolase/Barbiturase, repeating unit C / Cyanuric acid hydrolase/Barbiturase, repeating unit A / Amidohydrolase ring-opening protein (Amido_AtzD_TrzD) / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BARBITURIC ACID / Cyanuric acid amidohydrolase
Similarity search - Component
Biological speciesAzorhizobium caulinodans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.702 Å
AuthorsCho, S. / Shi, K. / Aihara, H.
CitationJournal: Plos One / Year: 2014
Title: Cyanuric acid hydrolase from Azorhizobium caulinodans ORS 571: crystal structure and insights into a new class of Ser-Lys dyad proteins.
Authors: Cho, S. / Shi, K. / Seffernick, J.L. / Dodge, A.G. / Wackett, L.P. / Aihara, H.
History
DepositionNov 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanuric acid amidohydrolase
B: Cyanuric acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,88918
Polymers73,4712
Non-polymers1,41816
Water3,099172
1
A: Cyanuric acid amidohydrolase
B: Cyanuric acid amidohydrolase
hetero molecules

A: Cyanuric acid amidohydrolase
B: Cyanuric acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,77936
Polymers146,9434
Non-polymers2,83632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area16010 Å2
ΔGint-367 kcal/mol
Surface area40980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)237.866, 237.866, 105.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

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Components

#1: Protein Cyanuric acid amidohydrolase


Mass: 36735.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azorhizobium caulinodans (bacteria) / Strain: ATCC 43989 / DSM 5975 / ORS 571 / Gene: AZC_3892 / Production host: Escherichia coli (E. coli) / References: UniProt: A8IKD2
#2: Chemical ChemComp-BR8 / BARBITURIC ACID


Mass: 128.086 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4N2O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 5.07 Å3/Da / Density % sol: 75.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1M MgSO4, Tris, pH 7.0 - 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
PH range: 7.0 - 7.5

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97864 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 15, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 42770 / Num. obs: 42770 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.75 Å / % possible all: 94.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.702→40.794 Å / SU ML: 0.22 / σ(F): 1.33 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 3168 5.37 %Random
Rwork0.1594 ---
all0.1611 39742 --
obs0.1611 36574 74.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.702→40.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4953 0 80 172 5205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095096
X-RAY DIFFRACTIONf_angle_d1.1886906
X-RAY DIFFRACTIONf_dihedral_angle_d12.8231787
X-RAY DIFFRACTIONf_chiral_restr0.045795
X-RAY DIFFRACTIONf_plane_restr0.005901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7019-2.74220.257110.2477201X-RAY DIFFRACTION6
2.7422-2.78510.3352250.2714436X-RAY DIFFRACTION13
2.7851-2.83070.3512490.2577897X-RAY DIFFRACTION27
2.8307-2.87950.314770.291332X-RAY DIFFRACTION41
2.8795-2.93190.2704980.25541724X-RAY DIFFRACTION52
2.9319-2.98820.30441070.24871890X-RAY DIFFRACTION58
2.9882-3.04920.31521150.24182008X-RAY DIFFRACTION62
3.0492-3.11550.24121330.20222351X-RAY DIFFRACTION72
3.1155-3.18790.22011380.20062451X-RAY DIFFRACTION75
3.1879-3.26760.22621510.18962592X-RAY DIFFRACTION80
3.2676-3.35590.24341530.18492687X-RAY DIFFRACTION83
3.3559-3.45460.19241670.18162807X-RAY DIFFRACTION86
3.4546-3.56610.16491680.16832871X-RAY DIFFRACTION89
3.5661-3.69350.1631700.15993000X-RAY DIFFRACTION92
3.6935-3.84120.23681670.15743065X-RAY DIFFRACTION93
3.8412-4.01590.16341730.14193100X-RAY DIFFRACTION96
4.0159-4.22740.19381750.12693153X-RAY DIFFRACTION97
4.2274-4.4920.14821850.12063182X-RAY DIFFRACTION98
4.492-4.83830.15051810.11843176X-RAY DIFFRACTION98
4.8383-5.32430.16951800.1293199X-RAY DIFFRACTION99
5.3243-6.09250.2131800.1513259X-RAY DIFFRACTION99
6.0925-7.66760.16071830.14443246X-RAY DIFFRACTION100
7.6676-40.79830.1571820.15123247X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.1015-3.4215-4.79215.98712.94517.6451-0.12320.4554-0.558-0.5131-0.14010.36310.3955-0.0590.28590.33850.0102-0.10830.4712-0.09080.2261152.169354.758735.1298
20.93530.93040.71662.9013-0.4511.24780.07450.13060.09720.32370.03340.24170.085-0.2007-0.09290.19490.07920.04330.22290.00820.1356157.265967.700447.3287
35.3253-1.8002-2.00818.2908-1.16225.11420.1643-0.2660.28460.32880.164-0.6414-0.14160.4918-0.33260.25610.0721-0.01040.1956-0.11140.2164167.282262.901447.5254
46.2499-2.59854.91393.9364-0.54434.84480.08410.7899-0.1368-0.49390.4606-0.80470.84451.1993-0.55490.47860.19120.0260.5357-0.01550.3178169.230961.966639.6482
51.2135-0.7096-0.74721.08730.7160.6279-0.0223-0.15950.15620.03260.11130.1822-0.0361-0.1511-0.03290.17080.13060.01620.26890.07950.2182151.772970.273143.7367
66.27515.67713.56665.28183.89495.09040.46051.1855-2.12440.17730.3721-0.98982.02240.28-0.82140.61560.1146-0.20920.4668-0.17780.6661157.250350.64732.8308
73.7552.0774-0.0235.6578-0.63721.70980.11840.3141-0.0905-0.0825-0.0039-0.35440.1071-0.0559-0.12170.18050.0781-0.01740.36020.05290.0437161.88572.603129.9463
80.43890.53830.08415.33313.57834.3157-0.10920.13280.0087-0.3517-0.0096-0.186-0.05130.70260.14530.22040.07430.02070.4180.10790.1283162.937783.058423.9538
92.43192.53811.90196.31753.66095.8183-0.13640.63230.0261-0.83350.2353-0.0090.12780.0002-0.05250.29480.1073-0.00090.47410.01670.1232159.988167.65422.3823
104.43291.43322.17774.92671.23056.2664-0.00510.6749-0.166-0.85240.05530.50390.1326-0.5946-0.050.35090.0541-0.1510.51620.04630.2496150.493767.824324.505
115.7494.6202-2.12328.8546-1.96563.53110.37590.05580.31280.1761-0.4853-0.6241-0.66490.49370.20230.29520.0369-0.03730.26490.17950.3172167.619489.691437.5361
121.10651.553-0.81043.7106-2.86856.4955-0.09190.42690.6628-0.2157-0.07230.0967-0.5423-0.07190.16980.38360.1451-0.01890.32520.15870.4256159.696593.095435.2907
133.7781-2.03012.71344.9104-1.5252.2126-0.1752-0.4096-0.05290.2530.12130.0104-0.0811-0.19110.05770.17620.1026-0.02210.22970.10550.1794155.751885.521234.57
142.0057-1.71572.80397.0408-0.0387.0068-0.04310.56880.2185-0.8759-0.03030.0088-0.05340.44250.08410.26370.0447-0.04690.49930.06950.1556154.61778.512419.913
150.46910.00430.5760.5355-0.11240.7342-0.07860.08670.1768-0.2718-0.01110.2611-0.1347-0.07440.13620.2370.1383-0.05910.4010.14610.2347153.942682.636127.6626
161.8872-0.13450.22682.6364-1.36420.71970.02710.2291-0.1281-0.54740.07970.42760.2005-0.2826-0.08470.25130.0089-0.08630.486-0.04850.1866149.409463.857328.505
173.8534-1.34241.0365.37051.24912.32880.04590.2205-0.217-0.25070.0961.06720.057-0.8588-0.12320.20340.0231-0.02060.5950.04490.3858137.840469.618634.3325
183.07570.09812.82433.4376-0.00282.5961-0.07180.19120.4223-0.1407-0.14620.2879-0.05450.03020.20560.39130.30260.03390.63560.11670.3875135.912490.46835.5893
192.4198-0.352-0.1112.33490.41070.683-0.0056-0.06330.1575-0.0119-0.03070.2533-0.1212-0.20350.05230.18440.18560.05820.40810.04760.3222142.014679.081142.7361
203.3747-1.18170.74970.4375-0.4521.67810.0187-0.2179-0.1824-0.19370.03870.50850.0732-0.3863-0.0850.1510.0599-0.07060.52220.05130.2342142.301270.736530.571
214.5204-5.4721-1.38617.12022.86114.5565-0.3368-0.64140.24990.24520.09640.97930.0887-0.61350.25610.53770.3980.0041.34540.15921.1649108.231491.800543.89
220.1220.15820.03870.2641-0.01240.08450.02830.1020.0686-0.0683-0.08670.5121-0.1024-0.16620.02650.57640.54790.07180.79220.0850.7898124.665699.824848.0831
234.1903-1.4668-2.87852.54372.21963.22440.17010.2694-0.0177-0.302-0.0931-0.27530.17250.3227-0.09980.67660.4490.060.7062-0.02431.0512116.3372108.493551.3577
242.7635-0.18280.70462.5742-0.11190.4501-0.0715-0.15390.24890.112-0.01410.3304-0.0972-0.13530.09020.52570.41050.08080.68550.07420.6684125.426794.326349.9571
251.0112-0.54920.02250.7434-0.00120.0004-0.0659-0.00190.21120.1085-0.0550.3692-0.1393-0.32990.16820.61150.42660.25811.0446-0.02661.1247115.548993.32458.9389
265.1227-1.72930.03872.35132.02583.3032-0.4332-0.5888-0.34040.3866-0.17750.33170.4916-0.64240.6131.02410.35090.47291.1281-0.04870.8655121.663687.20373.6402
278.1867-0.0445-1.81472.2577-1.4783.1020.0005-0.58080.31730.2674-0.10720.30690.0656-0.06320.09070.75110.3380.41621.2983-0.07411.0579112.246288.465266.6766
286.57321.4898-1.38061.3366-0.61831.555-0.3924-0.2343-0.80920.08260.2907-0.5340.27930.19330.0860.77120.42880.40481.70380.20541.5477105.395284.388359.7143
298.0794-2.78093.45097.53340.92084.49760.02920.1182-0.63930.31790.07790.96060.0841-1.0192-0.09190.56240.34230.22311.43480.20971.1586111.70679.419356.3066
304.54650.15572.16030.01680.0351.1579-0.1373-0.19280.51120.0118-0.05090.131-0.1318-0.1580.18980.82830.48830.12720.78250.01460.7537130.128994.376664.9135
311.1271-1.2965-2.5844.38736.27869.8679-0.1423-0.39680.31280.37370.03890.4413-0.5112-0.7450.0981.14480.49180.32330.9202-0.00850.9726135.190498.614577.4154
325.5182-2.7207-0.81642.56871.93372.6629-0.0281-0.05410.24880.1970.0884-0.10880.10820.0847-0.08030.90770.44090.13230.61990.06890.5592136.231989.181369.6444
330.0971-0.21510.09730.58090.12541.2093-0.1344-0.0693-0.30830.2799-0.06060.6002-0.0286-0.62670.23010.5680.31980.26970.88780.04620.7431122.876783.262866.264
346.13181.08135.93510.20221.12046.21230.0022-0.43920.10960.2886-0.19030.36220.285-0.7210.19260.83670.13820.56811.33640.19071.2128118.744477.116372.5561
351.90420.4107-0.70530.64430.44371.1969-0.0709-0.0555-0.02520.1059-0.13550.23050.061-0.33470.1670.56080.27280.3220.85820.14960.7592125.732581.136363.7806
364.95730.8903-1.02221.52071.1161.55390.27260.39260.3582-0.1785-0.34850.4418-0.1649-0.16830.06570.85090.48270.27140.97270.02640.8398121.68195.437963.5896
370.53350.07620.68250.01060.0980.8727-0.0234-0.0142-0.3060.0207-0.09570.5833-0.0708-0.38310.12540.48840.3690.09771.32530.08041.3076106.289684.910449.5873
383.4033-2.14251.37261.8845-0.30661.1324-0.04030.67860.436-0.1779-0.20880.5475-0.2558-0.4040.27290.29660.08850.04691.03170.13980.9875120.486874.495544.903
391.21430.0305-0.17420.54930.25980.152-0.02480.11090.0490.0265-0.03620.2747-0.0702-0.24910.06210.20310.21430.10950.59570.08870.4415134.443579.133850.4703
402.7360.2991-1.03761.2261-0.13861.37660.2110.34550.2231-0.03210.03560.4481-0.1981-0.1825-0.23610.34340.19380.20530.79740.0440.768122.046578.223252.4474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:8)
2X-RAY DIFFRACTION2(chain A and resid 9:59)
3X-RAY DIFFRACTION3(chain A and resid 60:66)
4X-RAY DIFFRACTION4(chain A and resid 67:73)
5X-RAY DIFFRACTION5(chain A and resid 74:93)
6X-RAY DIFFRACTION6(chain A and resid 94:99)
7X-RAY DIFFRACTION7(chain A and resid 104:123)
8X-RAY DIFFRACTION8(chain A and resid 124:130)
9X-RAY DIFFRACTION9(chain A and resid 131:145)
10X-RAY DIFFRACTION10(chain A and resid 146:155)
11X-RAY DIFFRACTION11(chain A and resid 156:173)
12X-RAY DIFFRACTION12(chain A and resid 174:182)
13X-RAY DIFFRACTION13(chain A and resid 183:188)
14X-RAY DIFFRACTION14(chain A and resid 189:205)
15X-RAY DIFFRACTION15(chain A and resid 206:233)
16X-RAY DIFFRACTION16(chain A and resid 234:257)
17X-RAY DIFFRACTION17(chain A and resid 258:289)
18X-RAY DIFFRACTION18(chain A and resid 290:302)
19X-RAY DIFFRACTION19(chain A and resid 303:335)
20X-RAY DIFFRACTION20(chain A and resid 336:355)
21X-RAY DIFFRACTION21(chain B and resid 1:8)
22X-RAY DIFFRACTION22(chain B and resid 9:60)
23X-RAY DIFFRACTION23(chain B and resid 61:70)
24X-RAY DIFFRACTION24(chain B and resid 71:90)
25X-RAY DIFFRACTION25(chain B and resid 91:123)
26X-RAY DIFFRACTION26(chain B and resid 124:130)
27X-RAY DIFFRACTION27(chain B and resid 131:138)
28X-RAY DIFFRACTION28(chain B and resid 139:146)
29X-RAY DIFFRACTION29(chain B and resid 147:153)
30X-RAY DIFFRACTION30(chain B and resid 154:163)
31X-RAY DIFFRACTION31(chain B and resid 164:173)
32X-RAY DIFFRACTION32(chain B and resid 174:184)
33X-RAY DIFFRACTION33(chain B and resid 185:198)
34X-RAY DIFFRACTION34(chain B and resid 199:210)
35X-RAY DIFFRACTION35(chain B and resid 211:230)
36X-RAY DIFFRACTION36(chain B and resid 231:236)
37X-RAY DIFFRACTION37(chain B and resid 237:249)
38X-RAY DIFFRACTION38(chain B and resid 250:278)
39X-RAY DIFFRACTION39(chain B and resid 279:333)
40X-RAY DIFFRACTION40(chain B and resid 334:354)

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