[English] 日本語
Yorodumi
- PDB-3ojg: Structure of an inactive lactonase from Geobacillus kaustophilus ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more