[English] 日本語
Yorodumi
- PDB-4h5u: Structural insights into yeast Nit2: wild-type yeast Nit2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h5u
TitleStructural insights into yeast Nit2: wild-type yeast Nit2
ComponentsProbable hydrolase NIT2
KeywordsHYDROLASE / similar to mouse Nit2 / probable CN hydolase
Function / homology
Function and homology information


deaminated glutathione amidase / [acetyl-CoA carboxylase]-phosphatase activity / deaminated glutathione amidase activity / amide catabolic process / mitochondrion
Similarity search - Function
Uncharacterised protein family UPF0012, conserved site / Nit1/2, carbon-nitrogen hydrolase domain / Uncharacterized protein family UPF0012 signature. / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Deaminated glutathione amidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLiu, H. / Qiu, X. / Zhang, M. / Gao, Y. / Niu, L. / Teng, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2
Authors: Liu, H. / Gao, Y. / Zhang, M. / Qiu, X. / Cooper, A.J.L. / Niu, L. / Teng, M.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Structure summary
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 8, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable hydrolase NIT2
B: Probable hydrolase NIT2
C: Probable hydrolase NIT2
D: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,98918
Polymers153,6554
Non-polymers1,33414
Water14,124784
1
A: Probable hydrolase NIT2
hetero molecules

C: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3808
Polymers76,8282
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3740 Å2
ΔGint-30 kcal/mol
Surface area24030 Å2
MethodPISA
2
B: Probable hydrolase NIT2
hetero molecules

D: Probable hydrolase NIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,60910
Polymers76,8282
Non-polymers7828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area3890 Å2
ΔGint-30 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.262, 125.665, 77.674
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Probable hydrolase NIT2


Mass: 38413.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: J0706, NIT2, YJL126W / Production host: Escherichia coli (E. coli)
References: UniProt: P47016, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17.5% PEG4000, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97792 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 21, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97792 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 95100 / Num. obs: 95100 / % possible obs: 100 % / Observed criterion σ(I): 4.66
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 4.81 / Num. unique all: 4714 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASER2.1.4phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMS

1ems


Resolution: 1.92→48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20228 4767 5 %RANDOM
Rwork0.17078 ---
all0.1724 95100 --
obs0.1724 90290 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0.03 Å2
2--0.52 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.92→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9441 0 83 784 10308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.01310.0229767
X-RAY DIFFRACTIONr_angle_refined_deg1.15971.98213219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80551212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61724.376425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.946151730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1181563
X-RAY DIFFRACTIONr_chiral_restr0.0770.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217224
X-RAY DIFFRACTIONr_mcbond_it0.4771.56033
X-RAY DIFFRACTIONr_mcangle_it0.88629759
X-RAY DIFFRACTIONr_scbond_it1.23733734
X-RAY DIFFRACTIONr_scangle_it2.1354.53449
LS refinement shellResolution: 1.92→1.967 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 320 -
Rwork0.207 6451 -
obs--96.3 %

+
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