[English] 日本語
Yorodumi
- PDB-5hy2: Structure-function analysis of functionally diverse members of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hy2
TitleStructure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes
ComponentsRing-opening amidohydrolase
KeywordsHYDROLASE / Toblerone fold / pyrimidine catabolism
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amides / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
Similarity search - Function
Cyanuric acid hydrolase/Barbituras, RU C / Cyanuric acid hydrolase/Barbiturase, RU A / Cyanuric acid hydrolase/Barbiturase / Cyanuric acid hydrolase/Barbiturase, repeating unit B / Cyanuric acid hydrolase/Barbiturase, repeating unit C / Cyanuric acid hydrolase/Barbiturase, repeating unit A / Amidohydrolase ring-opening protein (Amido_AtzD_TrzD) / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclic amide hydrolase
Similarity search - Component
Biological speciesFrankia sp. Eul1b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPeat, T.S. / Balotra, S. / Wilding, M. / Newman, J. / Scott, C.
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes.
Authors: Peat, T.S. / Balotra, S. / Wilding, M. / Hartley, C.J. / Newman, J. / Scott, C.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ring-opening amidohydrolase
B: Ring-opening amidohydrolase


Theoretical massNumber of molelcules
Total (without water)84,2072
Polymers84,2072
Non-polymers00
Water55831
1
A: Ring-opening amidohydrolase
B: Ring-opening amidohydrolase

A: Ring-opening amidohydrolase
B: Ring-opening amidohydrolase


Theoretical massNumber of molelcules
Total (without water)168,4144
Polymers168,4144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8530 Å2
ΔGint-78 kcal/mol
Surface area49740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.297, 72.750, 133.054
Angle α, β, γ (deg.)90.00, 92.22, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 14 - 390 / Label seq-ID: 34 - 410

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Ring-opening amidohydrolase


Mass: 42103.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frankia sp. Eul1b (bacteria) / Plasmid: pET14b variant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: E3JD18, cyanuric acid amidohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein was at 2.7 mg/mL with added atrazine; reservoir was 22% PEG 3350, 86 mM sodium acetate; drops were 150 nL protein plus 140 nL reservoir plus 10 nL microseeds.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9707 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9707 Å / Relative weight: 1
ReflectionResolution: 2.6→46.6 Å / Num. obs: 27567 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 14
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HY0

5hy0


Resolution: 2.6→41.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.081 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.273 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24123 1354 4.9 %RANDOM
Rwork0.20217 ---
obs0.20403 26209 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-1.97 Å2
2--4.35 Å20 Å2
3----3.25 Å2
Refinement stepCycle: 1 / Resolution: 2.6→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 0 31 4750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194835
X-RAY DIFFRACTIONr_bond_other_d0.010.024683
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9596598
X-RAY DIFFRACTIONr_angle_other_deg1.474310732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8415665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99723.793174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88815699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9621532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215605
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021015
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.595.3732675
X-RAY DIFFRACTIONr_mcbond_other4.5875.3712674
X-RAY DIFFRACTIONr_mcangle_it7.2038.0263335
X-RAY DIFFRACTIONr_mcangle_other7.2038.0283336
X-RAY DIFFRACTIONr_scbond_it4.6445.7012160
X-RAY DIFFRACTIONr_scbond_other4.6435.7032161
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2418.4243264
X-RAY DIFFRACTIONr_long_range_B_refined11.56450.01220195
X-RAY DIFFRACTIONr_long_range_B_other11.56550.01520195
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 36002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 125 -
Rwork0.334 1875 -
obs--98.43 %

+
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