[English] 日本語
Yorodumi
- PDB-2xt0: Dehalogenase DPpA from Plesiocystis pacifica SIR-I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xt0
TitleDehalogenase DPpA from Plesiocystis pacifica SIR-I
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE / ALPHA-BETA HYDROLASE FOLD
Function / homology
Function and homology information


catalytic activity / membrane
Similarity search - Function
: / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Haloalkane dehalogenase, putative
Similarity search - Component
Biological speciesPLESIOCYSTIS PACIFICA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBogdanovic, X. / Palm, G.J. / Hinrichs, W.
Citation
Journal: Appl.Microbiol.Biotechnol. / Year: 2011
Title: Cloning, Functional Expression, Biochemical Characterization, and Structural Analysis of a Haloalkane Dehalogenase from Plesiocystis Pacifica Sir-1.
Authors: Hesseler, M. / Bogdanovic, X. / Hidalgo, A. / Berenguer, J. / Palm, G.J. / Hinrichs, W. / Bornscheuer, U.T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Putative Haloalkane Dehalogenase Dppa from Plesiocystis Pacifica Sir-I.
Authors: Bogdanovic, X. / Hesseler, M. / Palm, G.J. / Bornscheuer, U.T. / Hinrichs, W.
History
DepositionOct 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Derived calculations
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: HALOALKANE DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0085
Polymers32,6241
Non-polymers3844
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HALOALKANE DEHALOGENASE
hetero molecules

A: HALOALKANE DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,01710
Polymers65,2482
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2630 Å2
ΔGint-114.5 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.262, 108.501, 67.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein HALOALKANE DEHALOGENASE / DPPA DEHALOGENASE


Mass: 32624.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLESIOCYSTIS PACIFICA (bacteria) / Strain: SIR-I / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: A6G7B1, haloalkane dehalogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.5, 1.8M (NH4)2SO4, 5% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 4, 2009 / Details: OSMIC MULTILAYER OPTIC
RadiationMonochromator: OSMIC MULTILAYER OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→38.68 Å / Num. obs: 25613 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CrystalClearV.1.3.6data reduction
CrystalClearV.1.3.6data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDB

1edb


Resolution: 1.9→67.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.419 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE NUMBER OF UNIQUE REFLECTIONS FOR REFINEMENT IS 25826 AND FOR DATA PROCESSING 25613. THIS IS DUE TO A DIFFERENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE NUMBER OF UNIQUE REFLECTIONS FOR REFINEMENT IS 25826 AND FOR DATA PROCESSING 25613. THIS IS DUE TO A DIFFERENT RESOLUTION USED FOR REFINEMENT (1.9 A) AND PROCESSING (1.95 A).
RfactorNum. reflection% reflectionSelection details
Rfree0.24801 1375 5.1 %RANDOM
Rwork0.21931 ---
obs0.22081 25826 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 20 260 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222399
X-RAY DIFFRACTIONr_bond_other_d0.0010.021649
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9733271
X-RAY DIFFRACTIONr_angle_other_deg1.08533983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.32422.883111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97915354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.61520
X-RAY DIFFRACTIONr_chiral_restr0.1180.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.51487
X-RAY DIFFRACTIONr_mcbond_other0.3621.5599
X-RAY DIFFRACTIONr_mcangle_it1.63822389
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7293912
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0394.5880
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 84 -
Rwork0.456 1775 -
obs--91.71 %
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)
10.97130.41810.07541.2971-0.18121.83470.0066-0.0242-0.05370.0508-0.0321-0.08640.05250.14360.02550.08020.0023-0.00570.06920.00370.09840.497318.970551.5628
21.07210.28130.48090.5047-0.71061.5888-0.06970.05530.0413-0.00020.05590.0422-0.0647-0.07580.01370.11630.00970.00310.11750.00230.119530.107822.712141.815
31.5813-0.809-0.79123.45670.86111.78860.0694-0.0886-0.21790.1952-0.13760.3050.159-0.13690.06830.1347-0.0416-0.00240.135300.12527.168412.562660.9103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 164
2X-RAY DIFFRACTION2A165 - 226
3X-RAY DIFFRACTION3A227 - 297

+
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