[English] 日本語
Yorodumi
- PDB-4ob3: Crystal Structure of Nitrile Hydratase from Pseudonocardia thermo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ob3
TitleCrystal Structure of Nitrile Hydratase from Pseudonocardia thermophila : A Reference Structure to Boronic Acid Inhibition of Nitrile Hydratase
Components
  • Cobalt-containing nitrile hydratase subunit alpha
  • Cobalt-containing nitrile hydratase subunit beta
KeywordsLYASE / Nitrile Hydratase / Nulceophile
Function / homology
Function and homology information


nitrile catabolic process / nitrile hydratase activity / nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / cobalt ion binding / transition metal ion binding
Similarity search - Function
Nitrile hydratase, alpha subunit / Nitrile hydratase, beta subunit / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal ...Nitrile hydratase, alpha subunit / Nitrile hydratase, beta subunit / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, alpha chain / Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily / SH3 type barrels. - #50 / Electron transport accessory-like domain superfamily / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Cobalt-containing nitrile hydratase subunit alpha / Cobalt-containing nitrile hydratase subunit beta
Similarity search - Component
Biological speciesPseudonocardia thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsRui, W. / Salette, M. / Ruslan, S. / Richard, H. / Dali, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile.
Authors: Martinez, S. / Wu, R. / Sanishvili, R. / Liu, D. / Holz, R.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cobalt-containing nitrile hydratase subunit alpha
B: Cobalt-containing nitrile hydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8544
Polymers50,7032
Non-polymers1512
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-52 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.234, 65.234, 184.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-604-

HOH

21B-641-

HOH

31B-648-

HOH

-
Components

#1: Protein Cobalt-containing nitrile hydratase subunit alpha / L-NHase / L-nitrilase


Mass: 24119.553 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase alpha subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SID2, nitrile hydratase
#2: Protein Cobalt-containing nitrile hydratase subunit beta / L-NHase / L-nitrilase


Mass: 26583.645 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SID3, nitrile hydratase
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 276 K / Method: evaporation / pH: 7.5
Details: 1.4 M sodium citrate tribasic, 0.1 M HEPES, 20 mM Butaneboronic Acid, pH 7.5, EVAPORATION, temperature 276K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2012
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→53.96 Å / Num. all: 176494 / Num. obs: 35437 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.4
Reflection shellResolution: 1.92→2.03 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5090 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→41.585 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 1734 4.99 %Random
Rwork0.175 ---
obs0.1763 34736 96.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→41.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 7 460 3944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173655
X-RAY DIFFRACTIONf_angle_d1.0934967
X-RAY DIFFRACTIONf_dihedral_angle_d15.3841384
X-RAY DIFFRACTIONf_chiral_restr0.046513
X-RAY DIFFRACTIONf_plane_restr0.005657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9157-1.97210.23111190.18042356X-RAY DIFFRACTION85
1.9721-2.03570.24321420.17242788X-RAY DIFFRACTION99
2.0357-2.10850.22941520.17152771X-RAY DIFFRACTION100
2.1085-2.19290.23791340.17442796X-RAY DIFFRACTION100
2.1929-2.29270.23871370.17632810X-RAY DIFFRACTION100
2.2927-2.41360.2241450.17962824X-RAY DIFFRACTION100
2.4136-2.56480.21621460.17692807X-RAY DIFFRACTION100
2.5648-2.76280.22311490.18152803X-RAY DIFFRACTION99
2.7628-3.04070.26341690.1912826X-RAY DIFFRACTION99
3.0407-3.48050.16721760.16672788X-RAY DIFFRACTION99
3.4805-4.38430.15851280.15622646X-RAY DIFFRACTION90
4.3843-41.59470.16561370.1842787X-RAY DIFFRACTION91

+
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