[English] 日本語
Yorodumi
- PDB-6y9g: Crystal structure of putative ancestral haloalkane dehalogenase A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y9g
TitleCrystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)
ComponentsAncestral haloalkane dehalogenase AncHLD5
KeywordsHYDROLASE / Haloalkane dehalogenase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.748 Å
AuthorsChaloupkova, R. / Damborsky, J. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 Czech Republic
CitationJournal: Comput Struct Biotechnol J / Year: 2020
Title: Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics.
Authors: Babkova, P. / Dunajova, Z. / Chaloupkova, R. / Damborsky, J. / Bednar, D. / Marek, M.
History
DepositionMar 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ancestral haloalkane dehalogenase AncHLD5
B: Ancestral haloalkane dehalogenase AncHLD5


Theoretical massNumber of molelcules
Total (without water)68,8442
Polymers68,8442
Non-polymers00
Water3,171176
1
A: Ancestral haloalkane dehalogenase AncHLD5


Theoretical massNumber of molelcules
Total (without water)34,4221
Polymers34,4221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ancestral haloalkane dehalogenase AncHLD5


Theoretical massNumber of molelcules
Total (without water)34,4221
Polymers34,4221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.871, 51.365, 78.419
Angle α, β, γ (deg.)90.000, 94.070, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ancestral haloalkane dehalogenase AncHLD5


Mass: 34421.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.86 Å3/Da / Density % sol: 34.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 8000, magnesium chloride, Tris base

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.748→47.06 Å / Num. obs: 50947 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 2588 / CC1/2: 0.789

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K2A

4k2a


Resolution: 1.748→39.988 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.78
RfactorNum. reflection% reflection
Rfree0.2154 2528 4.96 %
Rwork0.1831 --
obs0.1847 50921 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.57 Å2 / Biso mean: 26.0117 Å2 / Biso min: 12.1 Å2
Refinement stepCycle: final / Resolution: 1.748→39.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 0 178 4723
Biso mean---29.55 -
Num. residues----570
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7482-1.78190.27791150.271250493
1.7819-1.81820.28961410.23612702100
1.8182-1.85780.27311470.222682100
1.8578-1.9010.25751400.1994272299
1.901-1.94850.2541360.2013268299
1.9485-2.00120.20321320.17842701100
2.0012-2.06010.25061300.18252722100
2.0601-2.12660.22991630.18182661100
2.1266-2.20260.21361610.16862700100
2.2026-2.29080.21541370.1793268799
2.2908-2.3950.22941300.18092706100
2.395-2.52130.24251640.18292671100
2.5213-2.67920.21881310.18222730100
2.6792-2.8860.22191370.1884270499
2.886-3.17630.20621330.1838271899
3.1763-3.63570.19391520.171268098
3.6357-4.57950.18741480.1644267597
4.5795-39.9880.20471310.1885274697

+
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