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- PDB-3ojg: Structure of an inactive lactonase from Geobacillus kaustophilus ... -

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Basic information

Entry
Database: PDB / ID: 3ojg
TitleStructure of an inactive lactonase from Geobacillus kaustophilus with bound N-butyryl-DL-homoserine lactone
ComponentsPhosphotriesterase
KeywordsHYDROLASE / (beta/alpha)8 barrel / lactonase
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
: / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsXue, B. / Chow, J.Y. / Tung, A. / Robinson, R.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Directed evolution of a thermostable quorum-quenching lactonase from the amidohydrolase superfamily
Authors: Chow, J.Y. / Xue, B. / Lee, K.H. / Tung, A. / Wu, L. / Robinson, R.C. / Yew, W.S.
History
DepositionAug 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1714
Polymers36,8791
Non-polymers2923
Water4,738263
1
A: Phosphotriesterase
hetero molecules

A: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3438
Polymers73,7582
Non-polymers5856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3450 Å2
ΔGint-16 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.269, 76.244, 134.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21A-392-

HOH

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Components

#1: Protein Phosphotriesterase


Mass: 36878.938 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-HL4 / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / N-butyryl-L-homoserine lactone


Mass: 171.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 49.61 % / Mosaicity: 0.5 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Tris, 20%(w/v) PEG 4000, 1.0mM ZnCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2008 / Details: Inter-Frame Total Dead Time: 5s
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 47658 / Num. obs: 45826 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.092 / Χ2: 1.282 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.635.40.4321120.667189.4
1.63-1.665.80.3620970.679189.1
1.66-1.695.80.30621200.726190.7
1.69-1.725.70.27621410.755190.3
1.72-1.765.70.22521990.746193.7
1.76-1.85.60.20522130.813193.7
1.8-1.855.50.16622400.823194.2
1.85-1.95.60.17722741.061197.3
1.9-1.955.50.13823041.228197.3
1.95-2.025.60.11722971.205197.7
2.02-2.095.60.11123461.34198.7
2.09-2.175.70.09723381.357198.6
2.17-2.275.70.09123491.444198.9
2.27-2.395.80.08623641.397199
2.39-2.545.90.08623741.516199.5
2.54-2.745.70.08423851.634199.5
2.74-3.0160.07823851.676199.7
3.01-3.455.70.07824142.047199.6
3.45-4.3450.07723962.052198
4.34-505.30.10224782.168197.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.75 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å24.11 Å
Translation3.5 Å24.11 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→24.115 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8256 / SU ML: 0.22 / σ(F): 0.62 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 2302 5.04 %RANDOM
Rwork0.1969 ---
all0.198 47658 --
obs0.198 45678 95.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.959 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 93.83 Å2 / Biso mean: 26.8211 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.893 Å2-0 Å20 Å2
2---3.876 Å2-0 Å2
3---8.769 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 14 263 2820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052614
X-RAY DIFFRACTIONf_angle_deg1.0183536
X-RAY DIFFRACTIONf_chiral_restr0.065380
X-RAY DIFFRACTIONf_plane_restr0.005467
X-RAY DIFFRACTIONf_dihedral_angle_d17.045961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5997-1.65680.28882120.2623685389783
1.6568-1.72310.28442000.23974091429190
1.7231-1.80150.25052180.22464199441793
1.8015-1.89650.27422090.23144320452996
1.8965-2.01530.25452470.2114373462097
2.0153-2.17080.22542560.20754454471098
2.1708-2.3890.23232310.20124483471499
2.389-2.73430.21612400.19924538477899
2.7343-3.44340.20442410.19364570481199
3.4434-24.11770.18152480.16444663491198
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)
10.8908-0.25580.72220.267-0.42140.8923-0.15980.03090.70050.1451-0.0478-0.1769-0.65750.07940.14990.1512-0.0709-0.02860.1623-0.02030.365927.49127.162-23.7881
21.1392-0.02480.31970.12310.05850.12430.0470.05590.3286-0.0583-0.0737-0.0003-0.0448-0.01260.08820.14690.0008-0.00870.1364-0.04210.13263.4724-0.6765-23.3426
31.9982-1.24980.44812.04871.57082.8049-0.3146-0.44791.1320.0581-0.15260.4214-0.9266-0.37220.42030.32550.03310.00040.1778-0.16650.65250.264410.6441-20.6356
42.9213-1.1486-2.15851.97010.9722.2664-0.1865-0.81410.56560.6272-0.0420.18390.16460.1784-0.23290.1587-0.0116-0.00780.2381-0.21760.176712.11358.5245-11.2153
50.41720.1181-0.03470.0428-0.04250.11610.006-0.1270.33880.0436-0.0343-0.00270.0177-0.11620.05690.1771-0.0209-0.01470.1205-0.04290.202813.18292.495-24.3208
62.5454-0.5567-1.37771.0682-1.41994.2342-0.0973-0.03231.1344-0.11450.32960.3668-0.8861-0.4558-0.29640.2660.036-0.04770.1167-0.08020.521513.259814.2005-21.98
70.766-0.078-0.00450.0211-0.05760.2549-0.03890.03160.0719-0.066-0.0065-0.03210.0399-0.07850.02950.1613-0.01520.00020.10610.00430.154210.6335-4.2235-29.9726
83.6794-1.79750.99282.02250.69721.48920.11490.2602-0.79240.69920.02810.14360.23490.2781-0.18790.1653-0.0138-0.0470.0894-0.0040.1655.7476-11.8223-45.8406
91.7593-0.143-0.52160.8954-0.27120.48310.09710.4580.0617-0.1682-0.0192-0.29580.10990.046-0.00420.19-0.00490.01730.19740.01720.118316.3775-4.1783-42.6088
100.4722-0.07320.27650.94440.32030.5188-0.04070.0270.2430.03940.04350.2189-0.04660.06240.01650.1294-0.0162-0.00240.13240.02080.229816.25010.3788-32.8776
111.4739-0.5815-0.28770.3661-0.64994.6270.13860.2752-0.6494-0.4659-0.10130.08980.6356-0.13250.01210.20170.0164-0.0350.0855-0.0160.25211.1418-21.6405-32.3555
121.45270.02840.34411.01530.10590.0910.00970.4709-0.094-0.22280.0446-0.0290.1580.0216-0.03880.14560.01670.02690.15690.00390.101220.5348-9.9278-37.0431
131.35440.00020.50320.7535-0.34680.78640.1274-0.0321-0.21530.0539-0.0395-0.1173-0.10420.0457-0.09570.1610.0013-0.00270.15240.00890.150821.0994-17.4311-24.6191
141.7272-0.2132-0.33210.5102-0.40480.67310.187-0.344-0.41910.097-0.13370.118-0.1373-0.2404-0.0390.14790.0179-0.01350.2276-0.00820.096717.8421-14.9261-17.2058
151.31690.3918-0.48030.9548-0.61130.4379-0.1299-1.2116-0.52820.53930.29170.25510.0569-0.2353-0.0990.3464-0.014-0.00490.34320.08320.147515.7729-17.6507-6.9034
160.23470.06630.49650.54110.03791.0699-0.00470.05070.020.10710.1927-0.1912-0.0946-0.0706-0.10480.19920.0142-0.05620.2780.00440.165128.833-15.263-11.7456
172.4161-0.3818-0.24590.74380.27040.3801-0.1135-0.6360.04010.2420.10410.06290.12490.1135-0.04670.15890.00480.02740.1916-0.04110.07782.1721-4.7199-14.8103
181.8448-0.6630.26270.453-0.06460.1293-0.2401-0.8920.03360.25610.21290.11950.0162-0.1235-0.02480.2209-0.01070.02070.4102-0.04860.066312.2211-6.2231-5.515
193.13680.39240.76972.23681.18630.732-0.1905-0.99410.30280.7022-0.256-0.3153-0.26310.49830.33650.35010.0324-0.10780.595-0.04440.260929.1191-9.0078-0.8533
201.2812-0.16470.35281.10890.79841.1038-0.1009-0.32840.42610.2870.1623-0.14810.0335-0.2488-0.01960.1973-0.025-0.02460.1949-0.06060.239929.5466-3.7891-15.68
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

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