[English] 日本語
Yorodumi
- PDB-3s5c: Crystal Structure of a Hexachlorocyclohexane dehydrochlorinase (L... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s5c
TitleCrystal Structure of a Hexachlorocyclohexane dehydrochlorinase (LinA) Type2
ComponentsLinA
KeywordsTRANSFERASE / hexachlorocyclohexane dehydrochlorinase
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / LinA
Function and homology information
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKukshal, V. / Macwan, A.S. / Kumar, A. / Ramachandran, R.
CitationJournal: Plos One / Year: 2012
Title: Crystal structure of the hexachlorocyclohexane dehydrochlorinase (LinA-type2): mutational analysis, thermostability and enantioselectivity
Authors: Macwan, A.S. / Kukshal, V. / Srivastava, N. / Javed, S. / Kumar, A. / Ramachandran, R.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: LinA
A: LinA
C: LinA
D: LinA
E: LinA
F: LinA
G: LinA


Theoretical massNumber of molelcules
Total (without water)121,3487
Polymers121,3487
Non-polymers00
Water00
1
B: LinA

B: LinA

B: LinA


Theoretical massNumber of molelcules
Total (without water)52,0063
Polymers52,0063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6420 Å2
ΔGint-35 kcal/mol
Surface area17870 Å2
MethodPISA
2
A: LinA
C: LinA
E: LinA


Theoretical massNumber of molelcules
Total (without water)52,0063
Polymers52,0063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-40 kcal/mol
Surface area18980 Å2
MethodPISA
3
D: LinA
F: LinA
G: LinA


Theoretical massNumber of molelcules
Total (without water)52,0063
Polymers52,0063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-39 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.529, 162.529, 186.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein
LinA / Hexachlorocyclohexane dehydrochlorinase


Mass: 17335.467 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: The sequence was isolated from bacteria from a soil sample, metagenome source. It shows very high identity with the LinA from Sphingobium japonicum UT26 whose sequence is in PDB id: 3A76.
Source: (gene. exp.) uncultured organism (environmental samples)
Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5ANU3, Lyases; Carbon-halide lyases

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2% PEG 8000,0.1 M trisodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→30.72 Å / Num. all: 18690 / Num. obs: 18690 / % possible obs: 99.1 % / Observed criterion σ(F): 8.7 / Observed criterion σ(I): 8.7 / Rmerge(I) obs: 0.239
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2656 / % possible all: 98.5

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A76

3a76


Resolution: 3.5→30.72 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.839 / Occupancy max: 1 / Occupancy min: 1 / SU B: 31.762 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.662 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 969 5.2 %RANDOM
Rwork0.1788 ---
all0.1834 18669 --
obs0.1834 18669 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 105.35 Å2 / Biso mean: 50.1874 Å2 / Biso min: 18.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8266 0 0 0 8266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228472
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.93811526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69651042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.15324.296419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.256151326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2751549
X-RAY DIFFRACTIONr_chiral_restr0.090.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216593
X-RAY DIFFRACTIONr_mcbond_it0.491.55171
X-RAY DIFFRACTIONr_mcangle_it0.93728254
X-RAY DIFFRACTIONr_scbond_it0.97233301
X-RAY DIFFRACTIONr_scangle_it1.7444.53272
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 78 -
Rwork0.23 1245 -
all-1323 -
obs--97.71 %

+
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://pdbjlvh1.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