[English] 日本語
Yorodumi
- PDB-6kmo: Crystal structure of a novel esterase CinB from Enterobacter asburiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kmo
TitleCrystal structure of a novel esterase CinB from Enterobacter asburiae
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / Enterobacter asburiae / esterase / CinB
Function / homology
Function and homology information


Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / 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
Alpha/beta hydrolase
Similarity search - Component
Biological speciesEnterobacter asburiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsShang, F. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31200556 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural and functional analyses of the lipase CinB from Enterobacter asburiae.
Authors: Shang, F. / Lan, J. / Liu, W. / Chen, Y. / Wang, L. / Zhao, J. / Chen, J. / Gao, P. / Ha, N.C. / Quan, C. / Nam, K.H. / Xu, Y.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)72,7002
Polymers72,7002
Non-polymers00
Water16,412911
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-19 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.086, 89.396, 68.929
Angle α, β, γ (deg.)90.000, 111.256, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Alpha/beta hydrolase


Mass: 36350.105 Da / Num. of mol.: 2 / Mutation: V9I,T23A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter asburiae (bacteria) / Gene: AN689_0218030 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3AXI2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.16 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate PH 5.6, 22% (w/v) Polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979617 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979617 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 129477 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 8.79 Å2 / Rsym value: 0.072 / Net I/σ(I): 20.125
Reflection shellResolution: 1.45→1.48 Å / Num. unique obs: 12496 / Rsym value: 0.224

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→36.69 Å / SU ML: 0.0882 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 12.7926
RfactorNum. reflection% reflection
Rfree0.1512 1984 1.54 %
Rwork0.1273 --
obs0.1277 129082 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.11 Å2
Refinement stepCycle: LAST / Resolution: 1.45→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 1 911 5920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00775260
X-RAY DIFFRACTIONf_angle_d0.97797181
X-RAY DIFFRACTIONf_chiral_restr0.0751801
X-RAY DIFFRACTIONf_plane_restr0.0072951
X-RAY DIFFRACTIONf_dihedral_angle_d2.42584135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.17561430.15038650X-RAY DIFFRACTION95.06
1.49-1.530.15691310.13398971X-RAY DIFFRACTION98.66
1.53-1.570.14631370.12418995X-RAY DIFFRACTION98.76
1.57-1.620.13851440.12139039X-RAY DIFFRACTION99.05
1.62-1.680.13041400.11969080X-RAY DIFFRACTION99.35
1.68-1.750.15421340.11829060X-RAY DIFFRACTION99.49
1.75-1.830.15531540.11719089X-RAY DIFFRACTION99.76
1.83-1.920.14041270.12169122X-RAY DIFFRACTION99.76
1.92-2.040.15291540.12359132X-RAY DIFFRACTION99.9
2.04-2.20.15591360.12069092X-RAY DIFFRACTION99.96
2.2-2.420.14471510.1199149X-RAY DIFFRACTION99.92
2.42-2.770.14651380.12379168X-RAY DIFFRACTION99.94
2.77-3.490.13631480.13089165X-RAY DIFFRACTION99.79

+
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