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- PDB-4ha0: Structure of Geobacillus kaustophilus lactonase, mutant R230D wit... -

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Basic information

Entry
Database: PDB / ID: 4ha0
TitleStructure of Geobacillus kaustophilus lactonase, mutant R230D with Zn2+
ComponentsPhosphotriesterase
KeywordsHYDROLASE / (beta/alpha)8 barrel
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / catabolic process / hydrolase activity / zinc ion binding
Similarity search - Function
Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / HYDROXIDE ION / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.902 Å
AuthorsXue, B. / Chow, J.Y. / Yew, W.S. / Robinson, R.C.
CitationJournal: Biochemistry / Year: 2013
Title: Structural evidence of a productive active site architecture for an evolved quorum-quenching GKL lactonase.
Authors: Xue, B. / Chow, J.Y. / Baldansuren, A. / Yap, L.L. / Gan, Y.H. / Dikanov, S.A. / Robinson, R.C. / Yew, W.S.
History
DepositionSep 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9528
Polymers73,6762
Non-polymers2776
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-133 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.974, 76.218, 134.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 3:99 or resseq 108:144 or resseq...A0
211chain 'B' and (resseq 3:99 or resseq 108:144 or resseq...B0

NCS oper: (Code: given
Matrix: (-1, -0.000111, -1.75479), (-0.000111, 0.999999, -0.001411), (1.77051)
Vector: -34.988602, 0.026198, 67.353897)

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Components

#1: Protein Phosphotriesterase


Mass: 36837.820 Da / Num. of mol.: 2 / Mutation: R230D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1506 / Plasmid: pET-15b, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 293 K / Method: sitting-drop vapor diffusion / pH: 7.5
Details: 100 mM Tris, pH 7.5, 20% (w/v) PEG 4000, 10% (v/v) glycerol, 0.1 mM ZnCl2, sitting-drop vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.311 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.311 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 56082 / Num. obs: 56082 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.104 / Χ2: 2.083 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.935.90.40627860.582199.3
1.93-1.976.20.43827780.657198.9
1.97-2.016.30.35828350.745199.1
2.01-2.056.40.32128230.892199.9
2.05-2.096.40.2927990.996199.2
2.09-2.146.30.25928141.145199.1
2.14-2.196.20.23828021.264198.8
2.19-2.256.10.20628191.353198.7
2.25-2.326.10.20228031.527199.2
2.32-2.3960.18127991.626198
2.39-2.485.90.16327751.718197.8
2.48-2.585.80.14728022.036197.5
2.58-2.75.70.13227462.131196.2
2.7-2.845.50.11927862.335197.6
2.84-3.025.50.10127812.411196.8
3.02-3.255.40.09127542.982195.7
3.25-3.575.30.08627613.867195.1
3.57-4.095.20.08428064.815195.8
4.09-5.155.30.08227875.473194.5
5.15-305.50.07630264.973197.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.97 Å
Translation3.5 Å19.97 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→19.977 Å / Occupancy max: 1 / Occupancy min: 0.8 / SU ML: 0.28 / σ(F): 0 / Phase error: 38.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3032 2845 5.09 %random
Rwork0.2589 ---
all0.2611 55872 --
obs0.2611 55872 97.45 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.052 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 153.28 Å2 / Biso mean: 46.9088 Å2 / Biso min: 12.95 Å2
Baniso -1Baniso -2Baniso -3
1--5.0568 Å20 Å20 Å2
2--1.8358 Å2-0 Å2
3---6.8601 Å2
Refinement stepCycle: LAST / Resolution: 1.902→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 6 283 5369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095198
X-RAY DIFFRACTIONf_angle_d1.1947036
X-RAY DIFFRACTIONf_chiral_restr0.079758
X-RAY DIFFRACTIONf_plane_restr0.006930
X-RAY DIFFRACTIONf_dihedral_angle_d16.5661924
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2330X-RAY DIFFRACTIONPOSITIONAL0.032
12B2330X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9018-1.93450.37151350.32062611274698
1.9345-1.96970.35291550.32852627278299
1.9697-2.00750.36831530.30452670282399
2.0075-2.04850.31761450.289926752820100
2.0485-2.0930.351420.29062653279599
2.093-2.14160.38021510.28622646279799
2.1416-2.19510.30581320.27662678281099
2.1951-2.25440.2971400.27542673281399
2.2544-2.32060.30971500.26952649279999
2.3206-2.39540.28151440.26962633277798
2.3954-2.48090.33791240.26922665278998
2.4809-2.580.32931510.27582653280497
2.58-2.69710.31941450.26642598274396
2.6971-2.8390.31131540.26632623277798
2.839-3.01630.34631370.26472639277697
3.0163-3.24820.33881300.2622617274796
3.2482-3.57350.31521300.26262631276195
3.5735-4.08670.26151420.23842644278696
4.0867-5.13430.23631300.21712656278695
5.1343-19.9780.28721550.24662786294195
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)
10.1062-0.12550.07280.1667-0.1110.0854-0.01660.1692-0.0297-0.0537-0.0699-0.00460.0711-0.0141-0.27360.25640.08720.07840.7436-0.64010.73379.9299-45.364323.7987
20.005-0.0170.00730.11480.02190.45640.09710.1928-0.04570.10630.0576-0.0190.05790.3036-0.17140.30970.0317-0.06040.7075-0.45680.5202-14.0133-37.544823.4577
30.02030.0068-0.00820.0305-0.01830.0114-0.0076-0.02520.00440.01850.0065-0.0114-0.02670.005-0.02840.48650.0203-0.14520.7932-0.53190.7268-17.0245-48.899520.6334
40.0325-0.0009-0.01720.0402-0.01590.0665-0.01160.1462-0.0217-0.0423-0.01590.0386-0.01140.0933-0.09330.4696-0.00210.0651.4199-0.76180.7411-5.4505-46.983611.4245
50.1382-0.0215-0.11540.0971-0.05230.17950.04430.2827-0.18040.0072-0.0119-0.0007-0.01220.1322-0.01980.34930.0999-0.01780.5177-0.61640.7105-4.32-40.692724.4425
60.06650.0192-0.06190.1258-0.03860.0615-0.01970.0703-0.042-0.01690.00790.04850.05490.00220.00970.3547-0.1236-0.0010.6178-0.5550.6743-4.2668-52.426622.1782
70.7780.26640.32830.16760.0470.1947-0.00260.46-0.4119-0.20070.4493-0.31430.06560.44080.91240.2464-0.0025-0.04370.3571-0.25030.331-6.8576-34.065230.0668
80.0761-0.02580.0220.0085-0.00670.00640.10670.00540.0697-0.06120.0852-0.0328-0.09250.05230.02630.30120.0585-0.03320.2279-0.10250.3451-11.4526-26.329845.8754
90.13410.00350.02160.00910.02510.0355-0.08030.1394-0.1879-0.06860.0143-0.087-0.05720.0264-0.19620.16740.04720.01640.0735-0.28590.3228-0.9814-34.095842.6251
100.54790.15220.07950.07030.08220.1313-0.15340.32590.0487-0.12410.04230.1387-0.1424-0.1949-0.10450.2488-0.00380.050.3544-0.20190.4539-1.264-38.723532.9402
110.00810.0115-0.00640.0359-0.01530.00790.02640.02220.11-0.10120.14460.0674-0.0541-0.0074-0.00030.29640.0156-0.1120.35210.04220.6284-6.4173-16.66232.326
120.1372-0.10010.1510.1575-0.16210.19050.06450.1548-0.017-0.2518-0.0660.025-0.180.0655-0.26520.18650.0009-0.01120.3849-0.1009-0.12153.0543-28.364237.0918
130.09880.0578-0.03180.0763-0.06850.16370.12140.86550.2368-0.0980.0214-0.01110.0963-0.09330.03380.3432-0.0003-0.01380.6230.10090.67713.5835-20.780224.6795
140.07880.02260.01130.05320.02560.01970.13860.2696-0.131-0.0582-0.05020.2178-0.0169-0.1480.07910.2488-0.0419-0.01411.15170.02760.92290.3888-23.163517.1568
150.0011-0.0009-0.00090.00220.00420.00740.04270.02060.0406-0.05460.03890.0798-0.07040.08630.00040.72790.1404-0.15631.53530.06370.689-1.6234-20.56666.9656
160.06490.03470.11310.0796-0.01220.3389-0.05680.10190.0715-0.06940.09640.00960.0251-0.0208-0.00630.4030.0024-0.00791.3256-0.12960.777511.289-22.932711.7186
170.0674-0.09270.05720.4202-0.3690.3410.05470.2326-0.0523-0.1112-0.20110.09770.07050.2674-0.19320.48990.03540.04181.1139-0.44550.7072-15.3441-33.348714.8829
180.04620.10510.14060.26720.3410.4563-0.0720.20290.0152-0.11170.09880.0448-0.03390.16850.03270.46210.0694-0.03881.8176-0.29970.8795-5.2649-32.06045.5293
190.00320.00370.00520.00460.00840.017-0.10260.0052-0.0409-0.0119-0.1085-0.00620.02920.0096-0.00030.87250.0601-0.0781.4401-0.26680.758311.6446-29.27020.8437
200.00140.0038-0.00350.21410.02250.29280.01180.1369-0.00620.00940.03470.0314-0.0073-0.13220.190.45430.1414-0.08361.0449-0.33990.482812.0557-34.483515.7281
210.03970.07180.03860.14310.06090.0441-0.05850.1426-0.2513-0.14130.04430.03540.0672-0.02270.03920.11280.05770.1702-0.089-0.45910.6178-44.9136-45.335643.6157
220.0196-0.00980.02440.03-0.01310.0435-0.00290.1801-0.0831-0.20890.037-0.36370.05330.28420.02580.12060.10640.1542-0.2419-0.37450.098-20.9682-37.523143.9505
230.0379-0.0245-0.00770.01520.00530.0014-0.03940.0084-0.00450.0258-0.05710.0016-0.03810.0131-0.04010.3981-0.04050.04910.1419-0.01150.9832-17.9587-48.854946.789
240.0617-0.00580.04180.0073-0.00380.03280.05820.0114-0.141-0.03090.0683-0.1396-0.0512-0.02430.00410.24850.0220.03620.2040.05350.4276-29.5298-46.925255.9924
250.20860.0125-0.04490.10130.12180.1299-0.03990.2537-0.2216-0.2311-0.0423-0.115-0.20460.052-0.13920.1517-0.01120.0692-0.1816-0.25930.1089-30.6661-40.658642.9694
260.0529-0.0346-0.02980.05070.0540.0602-0.00620.0017-0.0577-0.04250.042-0.03160.05560.02710.07410.3573-0.04770.24780.0823-0.0720.6358-30.7162-52.378345.2483
270.11340.06240.0990.28890.01410.0929-0.14910.2308-0.0172-0.12690.0164-0.14820.00770.0647-0.16290.2211-0.00750.0429-0.004-0.19480.5692-28.1316-34.045937.34
280.02060.00450.01060.00160.00140.00560.13210.03030.05750.04860.04840.054-0.056-0.00220.00180.4476-0.02550.0980.6836-0.07790.5284-23.5339-26.324321.5144
290.11870.05510.29180.02870.14360.7284-0.01980.3728-0.0018-0.0968-0.09370.1331-0.20090.0204-0.24520.27890.0022-0.01630.5441-0.24710.5249-34.0032-34.089524.7697
300.09210.0243-0.02350.2178-0.16530.12450.0540.2087-0.36670.0911-0.0264-0.0073-0.01190.06130.22480.1696-0.0466-0.02970.193-0.21510.5003-33.7244-38.702534.4679
310.0305-0.02320.02280.0274-0.00040.0599-0.00110.04790.04760.0475-0.0041-0.031-0.0481-0.0132-0.00610.2651-0.1077-0.0410.27370.14830.3414-28.5695-16.643835.0514
320.07780.01860.05790.00750.00390.2076-0.21830.3450.0062-0.1131-0.2946-0.1637-0.16920.0038-0.10310.2953-0.0164-0.01520.30460.00330.7423-38.0394-28.351730.3019
331.8061-0.146-0.18540.5757-0.39780.32990.00880.6258-0.0687-0.33550.01330.1690.2572-0.09820.36610.0837-0.0160.0240.08850.06830.038-38.5722-20.756242.7038
340.53710.1262-0.49810.3371-0.15460.87270.13050.20710.132-0.1438-0.0250.0923-0.147-0.20370.24850.11440.00090.0325-0.00290.129-0.2175-35.3773-23.165250.226
350.2685-0.1298-0.03210.07340.02190.0080.0832-0.17580.11660.03180.0358-0.1283-0.0981-0.07160.04350.42420.0092-0.01060.2205-0.07270.1984-33.3643-20.511660.4167
360.08950.03490.00850.03860.0290.03030.02660.0885-0.0543-0.10340.1565-0.04280.13990.01080.10870.29170.06050.05760.2374-0.00850.1156-46.276-22.887655.6674
370.12750.05810.00590.06720.02980.1337-0.0272-0.0382-0.06430.01780.0356-0.05390.08-0.02980.0610.12760.0062-0.02850.1614-0.03040.0822-19.6914-33.467152.4625
380.0465-0.0567-0.04840.26150.14210.09310.0008-0.2626-0.01610.19650.1368-0.0712-0.1127-0.03310.18140.1849-0.0161-0.01960.26290.0440.0048-29.7099-32.010461.8754
390.0654-0.01790.06690.1025-0.04620.0753-0.0220.0538-0.0833-0.0341-0.04730.02960.0609-0.0606-0.15880.36770.00460.17720.3495-0.02120.1018-46.6319-29.204266.5486
400.1585-0.41790.03441.1444-0.07240.0370.03010.1702-0.2285-0.2012-0.04320.11590.0469-0.03540.03390.1502-0.02020.09650.0402-0.05780.4661-47.0417-34.438951.6775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:19)A3 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:41)A20 - 41
3X-RAY DIFFRACTION3(chain A and resid 42:47)A42 - 47
4X-RAY DIFFRACTION4(chain A and resid 48:61)A48 - 61
5X-RAY DIFFRACTION5(chain A and resid 62:81)A62 - 81
6X-RAY DIFFRACTION6(chain A and resid 82:87)A82 - 87
7X-RAY DIFFRACTION7(chain A and resid 88:109)A88 - 109
8X-RAY DIFFRACTION8(chain A and resid 110:114)A110 - 114
9X-RAY DIFFRACTION9(chain A and resid 115:131)A115 - 131
10X-RAY DIFFRACTION10(chain A and resid 132:149)A132 - 149
11X-RAY DIFFRACTION11(chain A and resid 150:155)A150 - 155
12X-RAY DIFFRACTION12(chain A and resid 156:175)A156 - 175
13X-RAY DIFFRACTION13(chain A and resid 176:217)A176 - 217
14X-RAY DIFFRACTION14(chain A and resid 218:240)A218 - 240
15X-RAY DIFFRACTION15(chain A and resid 241:248)A241 - 248
16X-RAY DIFFRACTION16(chain A and resid 249:262)A249 - 262
17X-RAY DIFFRACTION17(chain A and resid 263:282)A263 - 282
18X-RAY DIFFRACTION18(chain A and resid 283:302)A283 - 302
19X-RAY DIFFRACTION19(chain A and resid 303:310)A303 - 310
20X-RAY DIFFRACTION20(chain A and resid 311:325)A311 - 325
21X-RAY DIFFRACTION21(chain B and resid 3:19)B3 - 19
22X-RAY DIFFRACTION22(chain B and resid 20:41)B20 - 41
23X-RAY DIFFRACTION23(chain B and resid 42:47)B42 - 47
24X-RAY DIFFRACTION24(chain B and resid 48:61)B48 - 61
25X-RAY DIFFRACTION25(chain B and resid 62:81)B62 - 81
26X-RAY DIFFRACTION26(chain B and resid 82:87)B82 - 87
27X-RAY DIFFRACTION27(chain B and resid 88:109)B88 - 109
28X-RAY DIFFRACTION28(chain B and resid 110:114)B110 - 114
29X-RAY DIFFRACTION29(chain B and resid 115:131)B115 - 131
30X-RAY DIFFRACTION30(chain B and resid 132:149)B132 - 149
31X-RAY DIFFRACTION31(chain B and resid 150:155)B150 - 155
32X-RAY DIFFRACTION32(chain B and resid 156:175)B156 - 175
33X-RAY DIFFRACTION33(chain B and resid 176:217)B176 - 217
34X-RAY DIFFRACTION34(chain B and resid 218:240)B218 - 240
35X-RAY DIFFRACTION35(chain B and resid 241:248)B241 - 248
36X-RAY DIFFRACTION36(chain B and resid 249:262)B249 - 262
37X-RAY DIFFRACTION37(chain B and resid 263:282)B263 - 282
38X-RAY DIFFRACTION38(chain B and resid 283:302)B283 - 302
39X-RAY DIFFRACTION39(chain B and resid 303:310)B303 - 310
40X-RAY DIFFRACTION40(chain B and resid 311:325)B311 - 325

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