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- PDB-7y39: Ubiquitin-like domain of human ZFAND1 -

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Basic information

Entry
Database: PDB / ID: 7y39
TitleUbiquitin-like domain of human ZFAND1
ComponentsAN1-type zinc finger protein 1
KeywordsPROTEIN BINDING / ZFAND1 / p97 / proteasome / stress granule / ubiquitin-like domain / proteostasis
Function / homology
Function and homology information


positive regulation of intracellular protein transport / cellular response to arsenite ion / stress granule disassembly / proteasome binding / cytoplasmic stress granule / zinc ion binding / cytoplasm
Similarity search - Function
ZFAND1-like ubiquitin-like domain / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger
Similarity search - Domain/homology
AN1-type zinc finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsLai, C.H. / Ko, K.T. / Fan, P.J. / Yu, T.A. / Chang, C.F. / Draczkowski, P. / Hsu, S.T.D.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-001-050-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2811-M-001-583- Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2311-B-001-013-MY3 Taiwan
CitationJournal: To Be Published
Title: Structural Insight into ZFAND1 and p97 Interaction
Authors: Lai, C.H. / Ko, K.T. / Fan, P.J. / Yu, T.A. / Chang, C.F. / Draczkowski, P. / Hsu, S.T.D.
History
DepositionJun 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AN1-type zinc finger protein 1
B: AN1-type zinc finger protein 1


Theoretical massNumber of molelcules
Total (without water)31,3602
Polymers31,3602
Non-polymers00
Water2,090116
1
A: AN1-type zinc finger protein 1


Theoretical massNumber of molelcules
Total (without water)15,6801
Polymers15,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AN1-type zinc finger protein 1


Theoretical massNumber of molelcules
Total (without water)15,6801
Polymers15,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.158, 34.284, 64.522
Angle α, β, γ (deg.)90.000, 91.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AN1-type zinc finger protein 1 / Zinc finger AN1-type-containing protein 1


Mass: 15679.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZFAND1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TCF1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.73 Å3/Da / Density % sol: 29.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES (pH6.5), 1.2M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 17016 / % possible obs: 96 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.19 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.033 / Rrim(I) all: 0.059 / Χ2: 1.004 / Net I/σ(I): 12.5 / Num. measured all: 55773
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88-1.953.30.24416650.9760.1550.290.97196.3
1.95-2.033.30.18417060.9830.1180.220.97396.3
2.03-2.123.30.15316540.9880.0990.1830.99994.9
2.12-2.233.30.10316730.9930.0690.1251.00694.5
2.23-2.373.20.08916390.9930.060.1081.01894.6
2.37-2.553.20.0717080.9960.0470.0850.99796
2.55-2.813.30.0517260.9980.0340.0611.00297.2
2.81-3.213.30.03617300.9980.0250.0440.99597.7
3.21-4.053.30.02817340.9990.0190.0341.0896.2
4.05-303.20.04217810.9960.030.0521.00396.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.88 Å23.49 Å
Translation1.88 Å23.49 Å

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Processing

Software
NameVersionClassification
PHENIX1.20-4444refinement
HKL-2000data collection
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q8TCF1-F1

Resolution: 1.88→23.49 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 1705 10.06 %
Rwork0.2048 15237 -
obs0.2073 16942 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.76 Å2 / Biso mean: 28.1122 Å2 / Biso min: 13.92 Å2
Refinement stepCycle: final / Resolution: 1.88→23.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 116 2170
Biso mean---30.57 -
Num. residues----263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.940.29871360.26261201133792
1.94-20.24771410.22841268140996
2-2.070.26271390.23341252139196
2.07-2.150.24411390.21971266140594
2.15-2.250.27361370.2281210134794
2.25-2.370.24161450.21271244138995
2.37-2.520.27341380.22321281141996
2.52-2.710.24421510.21571289144097
2.71-2.990.25171400.22091282142297
2.99-3.420.21561460.19981306145297
3.42-4.30.17131490.1671308145796
4.3-23.490.22171440.19221330147495

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