[English] 日本語
Yorodumi
- PDB-2yxp: The Effect of Deuteration on Protein Structure A High Resolution ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yxp
TitleThe Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / protein deuteration / haloalkane dehalogenase / high resolution structure / catalytic mechanism
Function / homology
Function and homology information


1,2-dichloroethane catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
Similarity search - Function
Haloalkane dehalogenase, subfamily 1 / 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
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / rigid body refinement / Resolution: 1.53 Å
AuthorsLiu, X. / Hanson, L. / Langan, P. / Viola, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The effect of deuteration on protein structure: a high-resolution comparison of hydrogenous and perdeuterated haloalkane dehalogenase.
Authors: Liu, X. / Hanson, B.L. / Langan, P. / Viola, R.E.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Haloalkane dehalogenase


Theoretical massNumber of molelcules
Total (without water)35,1761
Polymers35,1761
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.666, 72.184, 41.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11X-659-

HOH

-
Components

#1: Protein Haloalkane dehalogenase /


Mass: 35175.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Gene: dhlA / Plasmid: pCH109 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22643, haloalkane dehalogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.4M ammonium sulfate, 0.1M MES,, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 2004
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.53→37.62 Å / Num. obs: 36268 / % possible obs: 0.99 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 6.12 % / Rsym value: 0.055 / Net I/σ(I): 17.5
Reflection shellResolution: 1.53→1.59 Å / Redundancy: 2.05 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1996 / Rsym value: 0.257 / % possible all: 0.48

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: rigid body refinement / Resolution: 1.53→37.62 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.584 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(I): 3.1 / ESU R: 0.092 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18477 1814 5 %RANDOM
Rwork0.15823 ---
obs0.15956 34454 85.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.281 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.53→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 0 399 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222552
X-RAY DIFFRACTIONr_bond_other_d0.0010.021738
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9563472
X-RAY DIFFRACTIONr_angle_other_deg0.89534214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8385309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83524.094127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8241515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_nbd_refined0.2310.2582
X-RAY DIFFRACTIONr_nbd_other0.1970.21924
X-RAY DIFFRACTIONr_nbtor_refined0.190.21269
X-RAY DIFFRACTIONr_nbtor_other0.0850.21191
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.243
X-RAY DIFFRACTIONr_mcbond_it0.971.52002
X-RAY DIFFRACTIONr_mcbond_other0.1591.5614
X-RAY DIFFRACTIONr_mcangle_it1.1522508
X-RAY DIFFRACTIONr_scbond_it1.9831201
X-RAY DIFFRACTIONr_scangle_it2.8534.5964
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 26 -
Rwork0.313 568 -
obs--19.03 %

+
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