[English] 日本語
Yorodumi
- PDB-7x8l: Microbial family VII carboxylesterase E93 Wild-type -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x8l
TitleMicrobial family VII carboxylesterase E93 Wild-type
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / Carboxylesterase / CPT11 / lipid metabolism / Erythrobacter
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function
: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Carboxylic ester hydrolase
Similarity search - Component
Biological speciesAltericroceibacterium indicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLi, Y. / Zhen, R. / Li, J. / Xu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31770004 China
CitationJournal: To Be Published
Title: Structural and functional insight into a marine microbial carboxylesterase E93
Authors: yang, L. / Zhen, R. / JiXi, L. / Xuewei, X.
History
DepositionMar 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)56,2751
Polymers56,2751
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19680 Å2
Unit cell
Length a, b, c (Å)44.850, 91.670, 110.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Carboxylic ester hydrolase


Mass: 56274.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Altericroceibacterium indicum (bacteria)
Gene: GRI39_13840 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A845ADQ8, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 mol/L BIS-TRIS, pH6.5 28% w/v PEG2000

-
Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.996 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 1.77→37.86 Å / Num. obs: 45341 / % possible obs: 99.65 % / Redundancy: 14.1 % / Biso Wilson estimate: 16.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09239 / Rpim(I) all: 0.02559 / Rrim(I) all: 0.09595 / Net I/σ(I): 23.91
Reflection shellResolution: 1.77→1.833 Å / Rmerge(I) obs: 0.6847 / Mean I/σ(I) obs: 6.44 / Num. unique obs: 4433 / CC1/2: 0.966 / Rpim(I) all: 0.1844 / Rrim(I) all: 0.7094

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4Y

1k4y


Resolution: 1.77→37.86 Å / SU ML: 0.1713 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.193 2000 4.41 %
Rwork0.1682 43341 -
obs0.1693 45341 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.97 Å2
Refinement stepCycle: LAST / Resolution: 1.77→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 0 274 4206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784075
X-RAY DIFFRACTIONf_angle_d1.00435571
X-RAY DIFFRACTIONf_chiral_restr0.0579599
X-RAY DIFFRACTIONf_plane_restr0.0079741
X-RAY DIFFRACTIONf_dihedral_angle_d5.6593558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.24761390.21253031X-RAY DIFFRACTION98.88
1.81-1.860.22321420.18913055X-RAY DIFFRACTION99.75
1.86-1.920.22271400.18753036X-RAY DIFFRACTION99.37
1.92-1.980.25471400.17863039X-RAY DIFFRACTION99.47
1.98-2.050.19991420.17653072X-RAY DIFFRACTION99.6
2.05-2.130.22751420.16913080X-RAY DIFFRACTION99.88
2.13-2.230.19941410.16323045X-RAY DIFFRACTION99.78
2.23-2.350.2181420.17353094X-RAY DIFFRACTION99.81
2.35-2.490.20421430.1773101X-RAY DIFFRACTION99.97
2.49-2.690.20311420.17853075X-RAY DIFFRACTION100
2.69-2.960.19191440.18253127X-RAY DIFFRACTION100
2.96-3.380.18291450.17143123X-RAY DIFFRACTION99.97
3.38-4.260.16991450.14783172X-RAY DIFFRACTION100
4.26-37.860.1591530.15173291X-RAY DIFFRACTION98.85

+
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