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- PDB-7d86: Crystal Structure of zebrafishPHF14-PZP -

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Basic information

Entry
Database: PDB / ID: 7d86
TitleCrystal Structure of zebrafishPHF14-PZP
ComponentsPHD finger protein 14
KeywordsGENE REGULATION / PHF14-PZP
Function / homology
Function and homology information


negative regulation of mesenchymal cell proliferation involved in lung development / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of mesenchymal cell proliferation / mesenchymal cell proliferation involved in lung development / mesenchymal cell proliferation / lung alveolus development / histone reader activity / histone binding / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II ...negative regulation of mesenchymal cell proliferation involved in lung development / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of mesenchymal cell proliferation / mesenchymal cell proliferation involved in lung development / mesenchymal cell proliferation / lung alveolus development / histone reader activity / histone binding / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type ...PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHD finger protein 14
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsLi, H. / Zheng, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14.
Authors: Zheng, S. / Bi, Y. / Chen, H. / Gong, B. / Jia, S. / Li, H.
History
DepositionOct 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7638
Polymers23,3491
Non-polymers4137
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.193, 41.907, 52.878
Angle α, β, γ (deg.)90.000, 98.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHD finger protein 14


Mass: 23349.238 Da / Num. of mol.: 1 / Fragment: PHF14-PZP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: phf14 / Plasmid: pSUMOH10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A286Y9D1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 37.81 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium chloride, 0.1 M Bis-Tris, 25 % v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2818 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 31, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2818 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 29554 / % possible obs: 98.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.05 / Rrim(I) all: 0.11 / Χ2: 2.971 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.934.30.7037330.8080.3640.7961.1998.3
1.93-1.974.20.66990.8510.3070.6771.2997.9
1.97-2.014.30.4627080.8930.2390.5231.37596.2
2.01-2.054.30.4117200.9240.2080.4631.43499
2.05-2.094.30.3536990.9380.180.3981.47296.3
2.09-2.144.30.2957300.9560.1510.3331.7299.2
2.14-2.194.30.2587050.9580.1320.2911.78497.6
2.19-2.254.20.2277070.9670.1160.2561.98398.6
2.25-2.324.30.2227510.9760.1140.2512.00798.3
2.32-2.394.30.197090.9710.0970.2152.1899
2.39-2.484.30.1867350.9730.0950.212.43397.9
2.48-2.584.30.1647210.9780.0850.1862.745100
2.58-2.74.30.1417250.9870.0710.1592.85498.5
2.7-2.844.20.1267390.9860.0650.1423.42498.7
2.84-3.024.20.1087290.9880.0560.1223.56999.3
3.02-3.254.20.0977220.9880.0510.114.13398.5
3.25-3.584.20.0757360.9920.040.0864.00799.1
3.58-4.094.10.0677190.9930.0350.0774.77297.2
4.09-5.164.30.0627450.9950.0310.075.41198.8
5.16-504.20.0787640.9910.040.0889.30797.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→41.68 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 2939 9.94 %
Rwork0.1744 26615 -
obs0.1793 29554 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.11 Å2 / Biso mean: 45.6136 Å2 / Biso min: 22.5 Å2
Refinement stepCycle: final / Resolution: 1.84→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 10 92 1535
Biso mean--41.25 44.85 -
Num. residues----185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.84-1.870.27841030.2718106180
1.87-1.90.30621360.2544128594
1.9-1.940.31831490.253124397
1.94-1.970.26861680.2568128696
1.97-2.010.25121510.2409124995
2.01-2.060.27191650.2151125696
2.06-2.10.25451260.2064130595
2.1-2.160.23251510.1986127598
2.16-2.220.21571180.2038132495
2.22-2.280.22231430.1892126297
2.28-2.350.23411480.1919129596
2.35-2.440.2091490.189125297
2.44-2.540.25491400.1865130596
2.54-2.650.22411460.1841128696
2.65-2.790.24761290.1661132796
2.79-2.970.1981440.1821125697
2.97-3.190.21691170.1821127795
3.19-3.520.21931580.1599128996
3.52-4.020.18361270.1392123794
4.03-5.070.17281300.1411129296
5.07-100.26781410.1653125393
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.56330.51220.85152.6964-0.22442.18270.0327-0.35520.05690.58-0.1201-0.1731-0.07090.03970.12810.3888-0.0169-0.04690.36410.0040.311311.1238-0.293818.8757
21.4661-0.830.62052.37470.40161.20060.04180.1021-0.1231-0.01170.0097-0.09520.13550.0267-0.05130.2624-0.01580.01170.2636-0.00590.293810.3405-3.08612.1339
31.4974-0.43480.27992.82470.29721.9117-0.0474-0.12620.09280.35550.0715-0.1207-0.09240.115-0.04340.28710.0040.0160.3024-0.01020.27034.028410.23577.9201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 284 through 377 )A284 - 377
2X-RAY DIFFRACTION2chain 'A' and (resid 378 through 440 )A378 - 440
3X-RAY DIFFRACTION3chain 'A' and (resid 441 through 485 )A441 - 485

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