[English] 日本語
Yorodumi
- PDB-4qa9: Ensemble refinement of an epoxide hydrolase from Streptomyces car... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qa9
TitleEnsemble refinement of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus.
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / Epoxide hydrolase / PSI-Biology
Function / homology
Function and homology information


ether hydrolase activity
Similarity search - Function
Epoxide hydrolase, N-terminal / Epoxide hydrolase N terminus / Epoxide hydrolase / Epoxide hydrolase-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsWang, F. / Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. ...Wang, F. / Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Joachimiak, A. / Phillips Jr., G.N. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: To be Published
Title: Ensemble refinement of an epoxide hydrolase from Streptomyces carzinostaticus subsp. neocarzinostaticus.
Authors: Wang, F. / Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Joachimiak, A. / Phillips Jr., G.N.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,35517
Polymers43,2261
Non-polymers1,12916
Water4,882271
1
A: Epoxide hydrolase
hetero molecules

A: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,71034
Polymers86,4522
Non-polymers2,25832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9250 Å2
ΔGint-65 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.330, 75.330, 165.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Number of models20
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

22A-505-

HOH

33A-683-

HOH

44A-567-

HOH

55A-545-

HOH

66A-533-

HOH

77A-524-

HOH

88A-516-

HOH

99A-510-

HOH

1010A-503-

HOH

1111A-619-

HOH

1212A-558-

HOH

1313A-542-

HOH

1414A-530-

HOH

1515A-521-

HOH

1616A-512-

HOH

1717A-506-

HOH

1818A-731-

HOH

1919A-568-

HOH

2020A-539-

HOH

-
Components

#1: Protein Epoxide hydrolase


Mass: 43225.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces carzinostaticus subsp. neocarzinostaticus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q84HB8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 2.0M ammonium sulfate and 0.1M Tris:HCl, pH 8.5. Cyro was ethylene glycol., VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2012
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.56→27.816 Å / Num. all: 66078 / Num. obs: 65946 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.56→1.59 Å / % possible all: 99.99

-
Processing

Software
NameVersionClassificationNB
PHENIXdev_1420refinement
PDB_EXTRACT3.14data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I19

4i19


Resolution: 1.56→27.816 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.151 3343 5.07 %same with 4i19
Rwork0.1219 ---
all0.1234 68419 --
obs0.1234 65942 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso min: 99999 Å2
Refinement stepCycle: LAST / Resolution: 1.56→27.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 68 271 3390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_plane_restr0.009
X-RAY DIFFRACTIONf_chiral_restr0.069
X-RAY DIFFRACTIONf_dihedral_angle_d9.95
X-RAY DIFFRACTIONf_angle_d1.216
X-RAY DIFFRACTIONf_bond_d0.009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5599-1.58210.22741200.2162162228282
1.5821-1.60570.221180.2022415253390
1.6057-1.63080.22851410.18462533267496
1.6308-1.65760.22191440.17392590273498
1.6576-1.68610.1941390.16712634277398
1.6861-1.71680.20171270.15052648277598
1.7168-1.74980.18481320.13262615274798
1.7498-1.78550.15641580.12092580273898
1.7855-1.82430.15791260.11512590271697
1.8243-1.86680.15161220.11152616273897
1.8668-1.91350.14141390.10852602274197
1.9135-1.96520.15641290.10812591272096
1.9652-2.0230.13621400.1032574271497
2.023-2.08830.13551310.10352648277996
2.0883-2.16290.13161350.09892568270396
2.1629-2.24940.13691290.0952585271496
2.2494-2.35180.12761480.09632567271595
2.3518-2.47570.10591540.09062620277497
2.4757-2.63070.14581580.09772604276296
2.6307-2.83360.14071600.1082632279297
2.8336-3.11840.1521450.12532736288199
3.1184-3.56890.17441480.13782758290699
3.5689-4.49330.15711520.12127882940100
4.4933-27.82080.13221480.14042943309199

+
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://pdbjlvh1.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