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- PDB-5zlq: Crystal Structure of C1orf123 -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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 %

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