[English] 日本語
Yorodumi
- PDB-3tn5: Crystal structure of GkaP mutant Y99L from Geobacillus kaustophil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tn5
TitleCrystal structure of GkaP mutant Y99L from Geobacillus kaustophilus HTA426
ComponentsPhosphotriesterase
KeywordsHYDROLASE / phosphotriesterase / 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
: / PHOSPHATE ION / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsAn, J. / Zhang, Z. / Zhang, Y. / Feng, Y. / Wu, G.
CitationJournal: to be published
Title: Engineering a thermostable lactonase for enhanced phosphotriesterase activity against organophosphate pesticides
Authors: An, J. / Zhang, Z. / Zhang, Y. / Feng, Y. / Wu, G.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphotriesterase
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3047
Polymers79,9732
Non-polymers3315
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-77 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.357, 80.295, 92.204
Angle α, β, γ (deg.)90.000, 99.350, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphotriesterase


Mass: 39986.461 Da / Num. of mol.: 2 / Mutation: Y99L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1506 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.35 Å3/Da / Density % sol: 47.56 % / Mosaicity: 0.367 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% PEG 20000, 0.1M MES pH6.5, vapor diffusion, hanging drop, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 74050

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.165 / SU ML: 0.09 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24928 3732 5 %RANDOM
Rwork0.22192 ---
obs-70261 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.19 Å2 / Biso mean: 27.3618 Å2 / Biso min: 12.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20.13 Å2
2---0.03 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 9 500 5597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225204
X-RAY DIFFRACTIONr_angle_refined_deg0.881.9627042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6025646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94923.76250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97715870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9671538
X-RAY DIFFRACTIONr_chiral_restr0.0570.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214014
X-RAY DIFFRACTIONr_mcbond_it0.1931.53210
X-RAY DIFFRACTIONr_mcangle_it0.3625158
X-RAY DIFFRACTIONr_scbond_it0.38531994
X-RAY DIFFRACTIONr_scangle_it0.6824.51884
LS refinement shellResolution: 1.752→1.798 Å / Total num. of bins used: 20
Num. reflection% reflection
Rfree262 -
Rwork5098 -
all5360 -
obs-97.97 %
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)
10.3160.0818-0.16710.5525-0.22290.801-0.0295-0.0267-0.0350.05390.03230.02990.0641-0.072-0.00280.0354-0.0054-0.00550.07030.01290.05597.8485-24.082135.0458
20.66760.104-0.09020.7344-0.18020.7927-0.00980.00710.0133-0.01270.011-0.0106-0.0743-0.0063-0.00120.0108-0.0001-0.00550.00020.00030.014829.0634-3.54339.7431
30.1046-0.2262-0.16470.4970.36490.2689-0.0164-0.009-0.01120.0370.00080.02250.0277-0.00560.01550.0291-0.0304-0.03610.06790.0420.055320.2318-13.711923.9969
40.22040.1127-0.13570.2322-0.12890.3203-0.0096-0.0085-0.0027-0.00470.0131-0.00070.0147-0.017-0.00350.07930.0054-0.01450.085-0.00140.09919.7-13.345620.6403
574.7162-112.064-72.8405236.339947.705126.5054-0.72550.32390.03770.31550.0325-0.88921.36-0.81090.6930.1628-0.00870.00950.2360.03120.13124.813-1.390816.5828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 326
2X-RAY DIFFRACTION2B3 - 326
3X-RAY DIFFRACTION3A327 - 328
4X-RAY DIFFRACTION3B327 - 328
5X-RAY DIFFRACTION4A329 - 576
6X-RAY DIFFRACTION4B330 - 581
7X-RAY DIFFRACTION5B329

+
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