[English] 日本語
Yorodumi
- PDB-6jsu: Structure of Geobacillus kaustophilus lactonase, Y99C/D266N doubl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jsu
TitleStructure of Geobacillus kaustophilus lactonase, Y99C/D266N double mutant
ComponentsPhosphotriesterase
KeywordsHYDROLASE / Alpha-Beta Barrel
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 hydrolase
Similarity search - Domain/homology
: / HYDROXIDE ION / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsXue, B. / Yew, W.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (Singapore) Singapore
CitationJournal: Structure / Year: 2020
Title: Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily.
Authors: Go, M.K. / Zhao, L.N. / Xue, B. / Supekar, S. / Robinson, R.C. / Fan, H. / Yew, W.S.
History
DepositionApr 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 17, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphotriesterase
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9148
Polymers73,6382
Non-polymers2776
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-136 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.600, 157.487, 50.618
Angle α, β, γ (deg.)90.000, 117.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphotriesterase


Mass: 36818.910 Da / Num. of mol.: 2 / Mutation: Y99C, D266N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: GK1506 / Plasmid: modified pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 467 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 17.00% w/v PEG 20000, 0.10 M TRIS-HCl, pH 8.5, 0.10 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→45.078 Å / Num. obs: 61214 / % possible obs: 98 % / Redundancy: 3.505 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.053 / Χ2: 1.159 / Net I/σ(I): 16.01 / Num. measured all: 421538
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.93.4950.2723.496589019932188550.9470.32194.6
1.9-2.043.4070.1565.876243018550183260.980.18698.8
2.04-2.23.5560.0999.646057817313170370.9920.11798.4
2.2-2.413.6320.07214.075732715940157860.9950.08499
2.41-2.693.5150.05518.655026414455142980.9960.06598.9
2.69-3.113.3750.04423.884218312684125000.9970.05298.5
3.11-3.83.6370.03632.313887710790106900.9980.04399.1
3.8-5.353.3970.03235.0827855834982010.9980.03898.2
5.35-45.0783.5330.0336.5316134469145670.9980.03597.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å29.65 Å
Translation3.5 Å29.65 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.7.17phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H9U

4h9u


Resolution: 1.8→19.873 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.25 / Phase error: 21.53
RfactorNum. reflection% reflection
Rfree0.1899 6382 5.32 %
Rwork0.1595 --
obs0.1612 60749 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 31.4311 Å2 / Biso min: 12.16 Å2
Refinement stepCycle: final / Resolution: 1.8→19.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 6 467 5547
Biso mean--20.91 40.06 -
Num. residues----646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125208
X-RAY DIFFRACTIONf_angle_d0.837022
X-RAY DIFFRACTIONf_chiral_restr0.053758
X-RAY DIFFRACTIONf_plane_restr0.006928
X-RAY DIFFRACTIONf_dihedral_angle_d3.5963094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.27292210.23633759398097
1.8205-1.84190.19931650.20623764392998
1.8419-1.86430.29982220.21083763398599
1.8643-1.88790.24981940.20893851404599
1.8879-1.91270.23371740.19143777395198
1.9127-1.93890.24822220.19743766398899
1.9389-1.96660.25312060.20873793399999
1.9666-1.99590.26922310.19483728395998
1.9959-2.0270.28011830.18863803398699
2.027-2.06020.2131710.1873840401198
2.0602-2.09570.23742140.18523746396098
2.0957-2.13380.22621970.17773823402099
2.1338-2.17480.20482360.17573751398799
2.1748-2.21910.21451750.174238534028100
2.2191-2.26730.24421800.17293843402399
2.2673-2.320.2212140.17543788400299
2.32-2.37790.20581940.16813818401299
2.3779-2.44210.23692280.177337894017100
2.4421-2.51380.19532610.16753734399599
2.5138-2.59480.20932510.16963753400499
2.5948-2.68730.22612520.17643724397699
2.6873-2.79460.2072890.17493792408199
2.7946-2.92140.19761830.17193750393399
2.9214-3.07490.19352090.15893793400299
3.0749-3.26680.17942240.152237703994100
3.2668-3.51770.19762140.150338124026100
3.5177-3.86940.16161960.13733847404399
3.8694-4.42390.1292490.12383752400199
4.4239-5.55350.14011880.12573790397898
5.5535-19.87390.14862390.13913763400299
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)
10.0381-0.05380.04420.087-0.06850.2378-0.0017-0.0395-0.03660.10020.1642-0.25820.04650.1040.13940.17960.04710.01890.2101-0.0780.269711.46732.395213.2908
20.19590.0635-0.08860.0234-0.04810.17160.0334-0.0849-0.04970.25210.059-0.04520.20510.14060.09350.45570.0794-0.03140.20310.00570.15196.81269.355231.4862
30.21740.1423-0.1190.0855-0.06180.1208-0.05120.00510.03920.18410.1891-0.12360.05610.20620.06570.1870.0656-0.03470.1964-0.04890.17489.507311.366520.5203
40.0644-0.09040.04530.1955-0.23170.9155-0.1020.1622-0.1258-0.08220.1793-0.1256-0.37110.12580.02820.1928-0.08390.04890.2302-0.06990.197213.368828.451111.4472
50.2536-0.16970.21350.34080.04590.3256-0.15020.0382-0.0523-0.13220.2428-0.2387-0.30930.12950.08120.1205-0.05010.01750.2088-0.04520.16578.244321.00199.6355
60.1624-0.1569-0.01010.50140.09930.0322-0.09650.0175-0.0906-0.32760.06860.1723-0.14040.0114-0.02320.1465-0.0278-0.01510.1806-0.00130.1213-4.031414.23094.813
70.0072-0.02650.01760.2396-0.15660.1012-0.0632-0.011-0.02060.12890.0360.2504-0.0471-0.1441-0.01550.1497-0.04140.05430.2402-0.00340.3362-13.11436.197715.279
80.2947-0.18540.06140.2407-0.00760.1439-0.0456-0.0071-0.14870.34630.11740.38380.0378-0.12620.11480.3099-0.01670.11910.19490.02760.2339-6.91063.671121.1002
90.00130.00190.00130.00310.00060.00490.02080.0013-0.1351-0.00880.05330.03090.16220.0749-00.21810.00630.01650.1968-0.03090.22211.3147-2.86666.6736
100.54360.15970.00570.065-0.07460.2255-0.0180.0405-0.01360.30020.1417-0.18360.12320.03910.14010.33880.0516-0.30.129-0.110.092617.401143.145245.8165
110.0098-0.01430.02730.0359-0.05040.0767-0.1270.03510.19710.01890.1649-0.24960.04580.0193-0.0506-0.2938-0.1045-0.12850.2253-0.18020.361322.927535.445128.0238
120.0320.0374-0.02590.116-0.07020.2826-0.1017-0.0018-0.0240.32450.21-0.22080.0977-0.03630.16010.18670.0325-0.10490.1871-0.05430.199415.157336.404636.5255
130.4316-0.3012-0.21040.21430.17730.3371-0.07860.095-0.09270.383-0.07350.16670.1087-0.102-0.1480.4326-0.04070.13290.1743-0.03070.1662-1.637126.344339.0619
140.01950.099-0.01120.4713-0.07790.01980.0040.0470.0390.28160.030.16860.2069-0.03190.01470.23060.0307-0.02730.16640.00340.13045.282435.110638.0756
150.3147-0.012-0.08520.0102-0.00050.025-0.05820.137-0.10210.3060.02950.25210.0419-0.04480.01550.2896-0.02920.13790.1839-0.00910.291-3.922335.499441.2568
160.34530.13930.29310.10950.09790.3424-0.10030.030.21060.1261-0.06820.3931-0.0517-0.031-0.08530.16370.00890.03190.1504-0.00270.2498-0.921849.849537.2496
170.0179-0.00750.0010.0058-0.00120.004-0.10420.18030.0945-0.2060.05220.077-0.0488-0.0607-0.00010.281-0.0695-0.0220.22090.02060.22568.986957.336327.1476
180.1088-0.05110.06870.2238-0.12710.3922-0.06560.18010.0591-0.09670.1146-0.1271-0.22790.1-0.01440.1795-0.0860.04470.2381-0.03280.217416.259252.448528.1269
190.00120.0012-0.00390.00380.00370.00750.00150.03360.17890.15850.053-0.07940.04530.1052-0.00010.28130.0011-0.03550.1943-0.02670.191613.718155.810645.5947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )A3 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 61 )A27 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 106 )A62 - 106
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 131 )A107 - 131
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 171 )A132 - 171
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 228 )A172 - 228
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 254 )A229 - 254
8X-RAY DIFFRACTION8chain 'A' and (resid 255 through 308 )A255 - 308
9X-RAY DIFFRACTION9chain 'A' and (resid 309 through 325 )A309 - 325
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 26 )B3 - 26
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 61 )B27 - 61
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 106 )B62 - 106
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 131 )B107 - 131
14X-RAY DIFFRACTION14chain 'B' and (resid 132 through 154 )B132 - 154
15X-RAY DIFFRACTION15chain 'B' and (resid 155 through 171 )B155 - 171
16X-RAY DIFFRACTION16chain 'B' and (resid 172 through 228 )B172 - 228
17X-RAY DIFFRACTION17chain 'B' and (resid 229 through 254 )B229 - 254
18X-RAY DIFFRACTION18chain 'B' and (resid 255 through 308 )B255 - 308
19X-RAY DIFFRACTION19chain 'B' and (resid 309 through 325 )B309 - 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