[English] 日本語
Yorodumi
- PDB-5zlq: Crystal Structure of C1orf123 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zlq
TitleCrystal Structure of C1orf123
ComponentsUPF0587 protein C1orf123
KeywordsMETAL BINDING PROTEIN / Zn-containing / Cys-X-X-Cys motif
Function / homologyCXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / zinc ion binding / CXXC motif containing zinc binding protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFurukawa, Y. / Lim, C.T. / Tosha, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H04768 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H05705 Japan
CitationJournal: PLoS ONE / Year: 2018
Title: Identification of a novel zinc-binding protein, C1orf123, as an interactor with a heavy metal-associated domain
Authors: Furukawa, Y. / Lim, C. / Tosha, T. / Yoshida, K. / Hagai, T. / Akiyama, S. / Watanabe, S. / Nakagome, K. / Shiro, Y.
History
DepositionMar 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0587 protein C1orf123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2882
Polymers18,2231
Non-polymers651
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8290 Å2
Unit cell
Length a, b, c (Å)118.131, 118.131, 118.131
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

21A-458-

HOH

-
Components

#1: Protein UPF0587 protein C1orf123


Mass: 18222.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1orf123 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NWV4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.83 Å3/Da / Density % sol: 67.88 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: Ammonium sulfate, Sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 1, 2015 / Details: MX225HE
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18717 / % possible obs: 99.9 % / Redundancy: 44.2 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.01 / Rrim(I) all: 0.067 / Χ2: 1.146 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0342.10.7279150.9750.1130.7350.847100
2.03-2.0742.70.649090.9820.0990.6480.862100
2.07-2.1142.90.4989470.9880.0770.5040.864100
2.11-2.1543.20.439320.9920.0660.4350.873100
2.15-2.243.80.3459380.9940.0530.3490.885100
2.2-2.2544.30.2699050.9960.0410.2720.926100
2.25-2.3144.50.2789350.9970.0420.2810.933100
2.31-2.3744.80.2429120.9970.0370.2450.907100
2.37-2.4445.10.1859420.9980.0280.1880.921100
2.44-2.52450.1639310.9990.0240.1640.94100
2.52-2.6145.30.1419500.9990.0210.1421.021100
2.61-2.7145.10.1229230.9990.0180.1241.209100
2.71-2.8445.50.1179290.9990.0170.1181.507100
2.84-2.99450.1069320.9990.0160.1081.881100
2.99-3.1745.20.0999380.9990.0150.12.103100
3.17-3.42450.0829440.9990.0120.0832.059100
3.42-3.76450.06193710.0090.0621.624100
3.76-4.3144.50.04496110.0070.0451.126100
4.31-5.4344.50.03695010.0050.0360.838100
5.43-5041.60.02698710.0040.0270.4798.2

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.69 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.284 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.142
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 898 5.1 %RANDOM
Rwork0.1803 ---
obs0.1831 16601 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.67 Å2 / Biso mean: 27.086 Å2 / Biso min: 4.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 1 175 1432
Biso mean--22.52 33.53 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191278
X-RAY DIFFRACTIONr_bond_other_d0.0030.021168
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.9541721
X-RAY DIFFRACTIONr_angle_other_deg1.0333.0032722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3485158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.325.55663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63515234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.276156
X-RAY DIFFRACTIONr_chiral_restr0.1270.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
LS refinement shellResolution: 1.999→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 63 -
Rwork0.221 1119 -
all-1182 -
obs--89.01 %

+
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