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- PDB-8jws: ePHD domain of PHD Finger Protein 7 (PHF7) -

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Basic information

Entry
Database: PDB / ID: 8jws
TitleePHD domain of PHD Finger Protein 7 (PHF7)
ComponentsPHD finger protein 7
KeywordsLIGASE / Ubiquitin / RING ligase / ePHD
Function / homology
Function and homology information


negative regulation of osteoclast proliferation / RING-type E3 ubiquitin transferase / nuclear speck / Golgi apparatus / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
PHF7/G2E3, PHD domain / PHF7/G2E3, ePHD domain / : / PHD-like zinc-binding domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase PHF7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBang, I. / Lee, H.S. / Choi, H.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Genes Dev. / Year: 2023
Title: Molecular basis for PHF7-mediated ubiquitination of histone H3.
Authors: Lee, H.S. / Bang, I. / You, J. / Jeong, T.K. / Kim, C.R. / Hwang, M. / Kim, J.S. / Baek, S.H. / Song, J.J. / Choi, H.J.
History
DepositionJun 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 7
B: PHD finger protein 7
C: PHD finger protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,98216
Polymers43,1453
Non-polymers83713
Water5,675315
1
A: PHD finger protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6405
Polymers14,3821
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHD finger protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6405
Polymers14,3821
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHD finger protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7026
Polymers14,3821
Non-polymers3205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.014, 59.145, 170.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 30 through 43 or resid 45...
d_2ens_1(chain "B" and (resid 30 through 43 or resid 45...
d_3ens_1(chain "C" and (resid 30 through 43 or resid 45...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDBeg label alt-IDEnd label alt-ID
d_11SERSERPROPROAA30 - 438 - 21
d_12LYSLYSSERSERAA45 - 6623 - 44
d_13LEULEUPROPROAA68 - 8346 - 61
d_14ASPASPVALVALAA85 - 9163 - 69
d_15ALAALALYSLYSAA93 - 9571 - 73
d_16ILEILELYSLYSAA97 - 10275 - 80
d_17GLYGLYPROPROAA105 - 14683 - 124
d_18ZNZNZNZNAD501LL
d_19ZNZNZNZNAE502LL
d_21SERSERPROPROBB30 - 438 - 21
d_22LYSLYSSERSERBB45 - 6623 - 44
d_23LEULEUPROPROBB68 - 8346 - 61
d_24ASPASPVALVALBB85 - 9163 - 69
d_25ALAALALYSLYSBB93 - 9571 - 73
d_26ILEILELYSLYSBB97 - 10275 - 80
d_27GLYGLYPROPROBB105 - 14683 - 124
d_28ZNZNZNZNBH501LL
d_29ZNZNZNZNBI502LL
d_31SERSERPROPROCC30 - 438 - 21
d_32LYSLYSSERSERCC45 - 6623 - 44
d_33LEULEUPROPROCC68 - 8346 - 61
d_34ASPASPVALVALCC85 - 9163 - 69
d_35ALAALALYSLYSCC93 - 9571 - 73
d_36ILEILELYSLYSCC97 - 10275 - 80
d_37GLYGLYPROPROCC105 - 14683 - 124
d_38ZNZNZNZNCL501LL
d_39ZNZNZNZNCM502LL

NCS oper:
IDCodeMatrixVector
1given(0.999957239146, -0.00834636215828, -0.00398222522414), (-0.00754969453407, -0.488100837494, -0.872754590105), (0.00534059841733, 0.872747334958, -0.48814297837)0.667935766686, 106.314899273, 67.2669197038
2given(0.999902505277, -9.14717732533E-5, -0.0139632222034), (0.0119713580386, -0.509139111584, 0.860600982827), (-0.00718794324546, -0.860684237504, -0.509088378166)1.16298435062, -6.32813832741, 126.796921629

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Components

#1: Protein PHD finger protein 7 / Testis development protein NYD-SP6


Mass: 14381.694 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Phf7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)PLysS / References: UniProt: Q9DAG9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.7 / Details: PEG 3350, LiCl, Bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2→31.01 Å / Num. obs: 25458 / % possible obs: 97 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.24 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.09503 / Rpim(I) all: 0.06078 / Rrim(I) all: 0.1132 / Net I/σ(I): 8.33
Reflection shellResolution: 2→2.072 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5245 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2513 / CC1/2: 0.712 / CC star: 0.912 / Rpim(I) all: 0.3391 / Rrim(I) all: 0.6268 / % possible all: 98.01

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NN2

4nn2


Resolution: 2→31.01 Å / SU ML: 0.1916 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.6664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 1333 5.25 %
Rwork0.1973 24081 -
obs0.1986 25414 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.07 Å2
Refinement stepCycle: LAST / Resolution: 2→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 25 315 3142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182877
X-RAY DIFFRACTIONf_angle_d1.23353845
X-RAY DIFFRACTIONf_chiral_restr0.0755387
X-RAY DIFFRACTIONf_plane_restr0.0085513
X-RAY DIFFRACTIONf_dihedral_angle_d15.51881135
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.560313601517
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.620305001266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.25671210.23432391X-RAY DIFFRACTION98.01
2.07-2.150.24211480.22182370X-RAY DIFFRACTION98.17
2.15-2.250.30081390.27262384X-RAY DIFFRACTION98.02
2.25-2.370.2881260.24632379X-RAY DIFFRACTION97.02
2.37-2.520.18961310.19682388X-RAY DIFFRACTION98.13
2.52-2.710.30191220.21072390X-RAY DIFFRACTION96.32
2.71-2.990.22761300.20952369X-RAY DIFFRACTION95.93
2.99-3.420.22761400.18982431X-RAY DIFFRACTION97.17
3.42-4.310.18961260.16392462X-RAY DIFFRACTION97.15
4.31-31.010.16831500.16382517X-RAY DIFFRACTION94.78
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)
13.679256004450.757014913557-0.7705347046371.53818827034-0.2596587766662.356346669620.04701624458820.0185443948380.08702656338780.0760238305855-0.03022069055990.0865059352517-0.001895711292250.0298288726671-0.02262486765710.1206698708690.0132769943742-0.002913219837760.05877308827010.009155561927380.085236464581132.999813008828.686360420380.2445851806
22.89043910235-0.1698306144150.1392997370911.311877168810.2716236673222.31516523633-0.007833620234850.345474044948-0.289428560522-0.0781099211195-0.01151647757550.04851194763820.0373285616646-0.01727050638580.006424700327760.136194487317-0.02368654537130.004113524881920.188819248806-0.06930485476780.14131782607733.123533956622.007740519753.2719841934
32.4138214432-0.667402093695-0.7008270310411.559144565720.4118905776732.088069316860.04042597681970.3127537683680.40694030417-0.0299286828180.04625049467140.0204998356158-0.0788777378358-0.182929009301-0.07074473201320.154564465584-0.0237813932511-0.01405865714080.1443005393950.08233883075070.19993631838633.084405453948.479849792861.030165358
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 30 - 146 / Label seq-ID: 1 - 117

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 30 through 146)AA
22(chain 'B' and resid 30 through 146)BE
33(chain 'C' and resid 30 through 146)CI

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