[English] 日本語
Yorodumi
- PDB-1jzt: Crystal structure of yeast ynu0, YNL200c -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jzt
TitleCrystal structure of yeast ynu0, YNL200c
ComponentsHypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
Keywordsstructural genomics / unknown function / yeast hypothetical protein / selenomethionine / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


: / NAD(P)H-hydrate epimerase / NAD(P)HX epimerase activity / nicotinamide nucleotide metabolic process / nucleotide binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
YjeF N-terminal domain-containing protein NAXE-like / YjeF N-terminal domain / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD(P)H-hydrate epimerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsJiang, J.-S. / Manning, N.O. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Yeast Hypothetical Protein YNU0_YEAST
Authors: Jiang, J.-S. / Manning, N.O. / Eswaramoorthy, S. / Gerchman, S.E. / Kumaran, D. / Kycia, J.H. / Lewis, H.A. / Swaminathan, S. / Studier, F.W.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 26, 2014Group: Other
Revision 1.4Feb 3, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_unobs_or_zero_occ_atoms ...audit_author / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _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 1.5Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
B: Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5544
Polymers55,4832
Non-polymers712
Water5,567309
1
A: Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7772
Polymers27,7411
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7772
Polymers27,7411
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-44 kcal/mol
Surface area20740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.732, 68.676, 125.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.017708, 0.578797, 0.815279), (0.568052, -0.6652, 0.484588), (0.822802, 0.471702, -0.317008)
Vector: 19.17647, 8.37586, -28.69405)

-
Components

#1: Protein Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region


Mass: 27741.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YNL200C / Plasmid: pET 13A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P40165
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.29 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium formate, PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9788, 0.9785, 0.9400
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: May 16, 2001 / Details: toroidal mirror
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97851
30.941
ReflectionResolution: 1.9→50 Å / Num. all: 40088 / Num. obs: 39366 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 5.8 / % possible all: 92.3

-
Processing

Software
NameClassification
ARP/wARPmodel building
SOLVEphasing
CNSrefinement
CCP4model building
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.94→46.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 165195.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
Details: LOOPS HAVE BEEN MODELLED IN AREAS OF POOR OR MISSING ELECTRON DENSITY. OCCUPANCY IS SET FOR LESS THAN 1 IN AREAS WHERE ELECTRON DENSITY IS AMBIGUOUS, AND IT IS SET EQUAL TO 0 WHERE ELECTRON ...Details: LOOPS HAVE BEEN MODELLED IN AREAS OF POOR OR MISSING ELECTRON DENSITY. OCCUPANCY IS SET FOR LESS THAN 1 IN AREAS WHERE ELECTRON DENSITY IS AMBIGUOUS, AND IT IS SET EQUAL TO 0 WHERE ELECTRON DENSITY IS NONEXISTENT. NOTE PARTICULARLY LOOPS A 119-A 123 AND B 120-B 123. THE FIRST THREE RESIDUES IN EACH CHAIN WERE NOT SEEN IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1786 5.1 %RANDOM
Rwork0.2 ---
obs0.2 34978 92.9 %-
all-34978 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.6171 Å2 / ksol: 0.392074 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---1.36 Å20 Å2
3---0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.94→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 2 309 4153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.882.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 275 5.3 %
Rwork0.188 4891 -
obs-4891 83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

+
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