[English] 日本語
Yorodumi
- PDB-7yii: Carboxylesterase - RoCE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yii
TitleCarboxylesterase - RoCE
ComponentsNon-heme haloperoxidase
KeywordsHYDROLASE / alpha/beta hydrolase / dimer / ester hydrolase / acyltransferase
Function / homology: / Alpha/beta hydrolase family / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / Alpha/beta hydrolase fold-1 / peroxidase activity / Alpha/Beta hydrolase fold / Non-heme haloperoxidase
Function and homology information
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsDou, Z. / Jia, P. / Ni, Y. / Xu, G.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22078127 China
CitationJournal: To Be Published
Title: Carboxylesterase - RoCE
Authors: Dou, Z. / Jia, P. / Ni, Y. / Xu, G.C.
History
DepositionJul 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 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: Non-heme haloperoxidase
B: Non-heme haloperoxidase


Theoretical massNumber of molelcules
Total (without water)56,8112
Polymers56,8112
Non-polymers00
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-13 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.677, 90.472, 131.358
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Non-heme haloperoxidase


Mass: 28405.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus opacus (bacteria) / Gene: R1CP_28090 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1B1KCC1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris buffer (pH 6.5), 25% PEG 300 (w/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.987 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.78→24.34 Å / Num. obs: 55437 / % possible obs: 98.5 % / Redundancy: 1 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 13.7
Reflection shellResolution: 1.78→1.82 Å / Rmerge(I) obs: 0.01 / Num. unique obs: 2642

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RNC

4rnc


Resolution: 1.78→24.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.988 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 2731 4.9 %RANDOM
Rwork0.1565 ---
obs0.158 52737 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.69 Å2 / Biso mean: 20.428 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.78→24.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 0 455 4422
Biso mean---34.57 -
Num. residues----546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134082
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153798
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.6275566
X-RAY DIFFRACTIONr_angle_other_deg1.5891.5768722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1565548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.4821.111198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61315578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1871532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02914
LS refinement shellResolution: 1.782→1.828 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 158 -
Rwork0.189 3309 -
all-3467 -
obs--84.11 %

+
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