[English] 日本語
Yorodumi
- PDB-4v2i: Biochemical characterization and structural analysis of a new col... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v2i
TitleBiochemical characterization and structural analysis of a new cold- active and salt tolerant esterase from the marine bacterium Thalassospira sp
ComponentsESTERASE/LIPASE
KeywordsHYDROLASE / THALIP2349
Function / homology
Function and homology information


methyl indole-3-acetate esterase activity / carboxylesterase
Similarity search - Function
Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTHALASSOSPIRA SP. GB04J01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.686 Å
AuthorsSanti, C.D. / Leiros, H.-K.S. / Scala, A.D. / Pascale, D.D. / Altermark, B. / Willassen, N.-P.
CitationJournal: Extremophiles / Year: 2016
Title: Biochemical Characterization and Structural Analysis of a New Cold-Active and Salt-Tolerant Esterase from the Marine Bacterium Thalassospira Sp.
Authors: De Santi, C. / Leiros, H.S. / Di Scala, A. / De Pascale, D. / Altermark, B. / Willassen, N.
History
DepositionOct 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ESTERASE/LIPASE
B: ESTERASE/LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9875
Polymers69,9142
Non-polymers733
Water16,682926
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-10.5 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.326, 85.429, 91.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ESTERASE/LIPASE / ESTERASE


Mass: 34956.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THALASSOSPIRA SP. GB04J01 THE STRAIN THALASSOSPIRA SP. GB04J01 WAS ISOLATED FROM A SEA FAN (PARAMURICEA PLACOMUS) DURING A RESEARCH-CRUISE WITH R/V HELMER HANSSEN TO THE VESTFJORDEN AREA ...Details: THALASSOSPIRA SP. GB04J01 THE STRAIN THALASSOSPIRA SP. GB04J01 WAS ISOLATED FROM A SEA FAN (PARAMURICEA PLACOMUS) DURING A RESEARCH-CRUISE WITH R/V HELMER HANSSEN TO THE VESTFJORDEN AREA (NORTHERN NORWAY AND IT IS PRESERVED AND AVAILABLE FROM AN IN-HOUSE COLLECTION AT THE UNIVERSITY OF TROMSO, NORWAY (DATABASE INDEX GB04J01).
Source: (gene. exp.) THALASSOSPIRA SP. GB04J01 (bacteria) / Plasmid: PET-26B-THAEST2349 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: A0A023T3X2, carboxylesterase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 926 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GENE CONTAINS A N-TERMINAL LEADER SEQUENCE (27 AMINO ACIDS LONG) THAT WAS NOT INCLUDED IN THE ...THE GENE CONTAINS A N-TERMINAL LEADER SEQUENCE (27 AMINO ACIDS LONG) THAT WAS NOT INCLUDED IN THE CLONING CONSTRUCT. GB KJ365310

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.22 % / Description: NONE
Crystal growpH: 8
Details: THE PROTEIN WAS AT 10 MG/ML IN 50 MM TRIS-HCL PH 8.0, 500 MM NACL AND 10% GLYCEROL. RESERVOIR: 25% PEG 3350, 0.2 M MGCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91705
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91705 Å / Relative weight: 1
ReflectionResolution: 1.69→25 Å / Num. obs: 61330 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 12.87 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.6
Reflection shellResolution: 1.69→1.79 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.4 / % possible all: 63.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZ3

1qz3


Resolution: 1.686→24.866 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 17.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1821 3064 5 %
Rwork0.1431 --
obs0.1451 61289 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.686→24.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 3 926 5707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084964
X-RAY DIFFRACTIONf_angle_d1.1776808
X-RAY DIFFRACTIONf_dihedral_angle_d12.8751772
X-RAY DIFFRACTIONf_chiral_restr0.045781
X-RAY DIFFRACTIONf_plane_restr0.006904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6858-1.712200.17374X-RAY DIFFRACTION0
1.7122-1.74020.25491020.22331925X-RAY DIFFRACTION95
1.7402-1.77020.22871470.19872794X-RAY DIFFRACTION100
1.7702-1.80240.25321470.19972797X-RAY DIFFRACTION100
1.8024-1.83710.22921480.19692818X-RAY DIFFRACTION100
1.8371-1.87450.2461460.20412779X-RAY DIFFRACTION100
1.8745-1.91530.26051450.2182754X-RAY DIFFRACTION99
1.9153-1.95980.25981460.21072758X-RAY DIFFRACTION98
1.9598-2.00880.18331470.15032790X-RAY DIFFRACTION100
2.0088-2.06310.17131480.14712811X-RAY DIFFRACTION100
2.0631-2.12380.19981460.14632779X-RAY DIFFRACTION99
2.1238-2.19230.17691480.13632815X-RAY DIFFRACTION100
2.1923-2.27060.21591420.16142720X-RAY DIFFRACTION96
2.2706-2.36140.16811490.13112813X-RAY DIFFRACTION100
2.3614-2.46880.16791480.12672818X-RAY DIFFRACTION100
2.4688-2.59890.16511480.1292819X-RAY DIFFRACTION100
2.5989-2.76150.16441490.12942829X-RAY DIFFRACTION100
2.7615-2.97440.18421500.13032847X-RAY DIFFRACTION100
2.9744-3.27310.18621500.13062858X-RAY DIFFRACTION100
3.2731-3.74540.16721510.11812853X-RAY DIFFRACTION99
3.7454-4.71350.13131520.10952893X-RAY DIFFRACTION99
4.7135-24.86870.1531550.13182951X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -20.3966 Å / Origin y: -39.6192 Å / Origin z: 11.973 Å
111213212223313233
T0.0854 Å20.0179 Å20.0105 Å2-0.1022 Å20.0125 Å2--0.0888 Å2
L0.3744 °20.2685 °2-0.0173 °2-0.5947 °2-0.0229 °2--0.295 °2
S0.0207 Å °-0.0125 Å °-0.0018 Å °0.0029 Å °-0.0424 Å °-0.0324 Å °0.0035 Å °0.0338 Å °0.0209 Å °
Refinement TLS groupSelection details: ALL

+
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