PDB-2faz: Ubiquitin-Like Domain of Human Nuclear Zinc Finger Protein NP95

ID or keywords:

Entry

Database: PDB / ID: 2faz

Title

Ubiquitin-Like Domain of Human Nuclear Zinc Finger Protein NP95

Components

Ubiquitin-like containing PHD and RING finger domains protein 1

Keywords

LIGASE /

Cell cycle /

DNA damage /

DNA repair / DNA-binding / Metal-binding /

Nuclear protein /

Phosphorylation / Polymorphism /

Transcription /

Transcription regulation / Ubl conjugation / Ubl conjugation pathway /

Zinc /

Zinc-finger /

STRUCTURAL GENOMICS CONSORTIUM / SGC

Function / homology

Function and homology information

histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding /

homologous recombination / negative regulation of gene expression via chromosomal CpG island methylation / regulation of epithelial cell proliferation / methyl-CpG binding /

mitotic spindle assembly ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Walker, J.R. / Wybenga-Groot, L. / Doherty, R.S. / Finerty Jr., P.J. / Newman, E. / Mackenzie, F.M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...

Citation

Journal: To be Published
Title: Ubiquitin-Like Domain of Human Nuclear Zinc Finger Protein NP95
Authors: Walker, J.R. / Wybenga-Groot, L. / Doherty, R.S. / Finerty Jr., P.J. / Newman, E. / Mackenzie, F.M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S.

History

Deposition	Dec 8, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 20, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2faz.cif.gz	47.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2faz.ent.gz	35.6 KB	Display	PDB format
PDBx/mmJSON format	2faz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fa/2faz ftp://data.pdbj.org/pub/pdb/validation_reports/fa/2faz	HTTPS FTP

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Related structure data

Related structure data	1sifS S: Starting model for refinement
Similar structure data	6tgj-1 2fq0-d 4pig-2 1ql4-1 6l0x-1 5zcz-d 4ow1-5 1eo0-d 4rtw-2 3hm3-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#116 - Aug 2009 Sulfotransferases similarity (1) #163 - Jul 2013 HIV Capsid similarity (2) #139 - Jul 2011 DNA Methyltransferase similarity (1) #56 - Aug 2004 Caspases similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Ubiquitin-like containing PHD and RING finger domains protein 1

B: Ubiquitin-like containing PHD and RING finger domains protein 1

18.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ubiquitin-like containing PHD and RING finger domains protein 1

defined by author
9.35 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ubiquitin-like containing PHD and RING finger domains protein 1

defined by author
9.35 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.554, 89.554, 108.279
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Ubiquitin-like containing PHD and RING finger domains protein 1 / Inverted CCAAT box binding protein of 90 kDa / Transcription factor ICBP90 / Nuclear zinc finger ...Inverted CCAAT box binding protein of 90 kDa / Transcription factor ICBP90 / Nuclear zinc finger protein Np95 / Nuclear protein 95 / HuNp95 / RING finger protein 106 Mass: 9346.675 Da / Num. of mol.: 2 / Fragment: UBIQUITIN-LIKE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Ubiquitin-like containing PHD and RING finger domains protein 1 / Inverted CCAAT box binding protein of 90 kDa / Transcription factor ICBP90 / Nuclear zinc finger ...

Mass: 9346.675 Da / Num. of mol.: 2 / Fragment: UBIQUITIN-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q96T88,

Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.35 Å³/Da / Density % sol: 63.31 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Well Solution: 20.0% P3350, 0.2 M tri-Li Citrate; Protein Buffer: 20 mM Tris pH 8.0, 100 mM NaCl, 5 mM beta- mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97868 Å
Detector	Type: SBC-3 / Detector: CCD / Date: Nov 30, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97868 Å / Relative weight: 1
Reflection	Resolution: 2→22.8 Å / Num. all: 17642 / Num. obs: 17642 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / R_merge(I) obs: 0.056 / Net I/σ(I): 28.67
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.626 / Mean I/σ(I) obs: 2.36 / Num. unique all: 1728 / % possible all: 99

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SIF

1sif

Resolution: 2→22.8 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.936 / SU B: 10.677 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25243	903	5.1 %	RANDOM
R_work	0.2179	-	-	-
obs	0.21959	16778	98.75 %	-
all	-	17642	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 36.319 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.39 Å²	1.2 Å²	0 Å²
2-	-	2.39 Å²	0 Å²
3-	-	-	-3.59 Å²

Refinement step

Cycle: LAST / Resolution: 2→22.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1273	0	0	80	1353

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.021	1293
X-RAY DIFFRACTION	r_angle_refined_deg	1.736	1.952	1735
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.356	5	149
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.643	22.778	72
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.002	15	255
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.912	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	191
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	967
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	538
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	867
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	84
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.211	0.2	27
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.185	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	1.946	3	772
X-RAY DIFFRACTION	r_mcangle_it	2.569	4	1210
X-RAY DIFFRACTION	r_scbond_it	4.148	5	581
X-RAY DIFFRACTION	r_scangle_it	5.914	7	525

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.33	79	-
R_work	0.253	1181	-
obs	-	-	97.67 %

Refinement TLS params.

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

ID	L11 (°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)
1	9.2934	3.0638	5.8067	17.757	5.4554	12.2571	-0.0853	-0.3264	-0.2798	0.3607	0.0382	0.0245	0.318	0.3531	0.0472	-0.1071	-0.0909	0.0145	0.186	-0.0351	0.0218	-18.1249	36.1125	-3.5741
2	15.2375	16.5558	10.544	35.6218	11.4285	16.7405	0.9017	-0.5587	0.1152	0.9847	-0.805	0.1353	0.5397	-0.7502	-0.0967	-0.1298	-0.1141	0.0331	0.3029	-0.034	0.0207	-14.0043	38.4459	1.3216
3	26.2687	18.445	3.3066	26.8432	5.952	13.8064	-0.1088	0.4448	0.351	0.0999	0.2471	0.4829	0.0562	0.5285	-0.1383	-0.1364	0.0032	0.0065	0.2154	0.0072	0.0422	-12.2487	36.7655	-1.8162
4	3.8747	3.8637	2.5447	4.6204	4.0433	26.962	-0.3345	0.0198	-0.3664	0.21	0.2822	0.5123	-0.2177	0.5589	0.0523	0.0333	-0.069	0.0341	0.1708	0.0477	0.1343	-22.242	32.6676	6.5913
5	19.3102	-0.9922	-10.7184	0.9548	1.0777	10.5968	0.832	-0.0944	0.905	0.2103	0.0427	-0.2228	-0.2034	-0.1037	-0.8746	0.0209	-0.0404	0.0532	0.2506	0.0429	0.104	-18.353	37.2725	8.5684
6	3.4729	-0.3891	1.2159	4.6078	0.9388	5.2876	-0.069	0.479	-0.0543	-1.2158	0.032	0.296	-0.3155	0.3661	0.0369	0.2215	-0.1824	-0.0368	0.0931	-0.0358	0.0433	-21.0324	41.5806	-11.2801
7	4.7183	5.0087	-5.3169	21.2945	-7.5239	12.2265	0.264	-0.5127	0.0281	0.3352	-0.1652	-0.2625	-0.347	0.5974	-0.0987	-0.1223	-0.0982	0.0087	0.2492	-0.0162	0.0438	-21.408	41.6314	8.662
8	5.1932	0.5454	-4.1262	6.348	-1.5884	15.3707	0.4327	-0.652	-0.1203	0.0704	-0.044	-0.0646	-0.3395	0.3751	-0.3887	-0.1031	-0.1201	0.0561	0.1692	-0.0015	0.0375	-25.3407	38.8313	7.0683
9	5.8154	1.0744	5.8478	1.2027	1.5413	14.4268	-0.0586	0.1767	-0.1942	-0.2779	0.2945	-0.1034	-0.1209	0.6912	-0.2359	-0.0969	-0.1212	0.0209	0.0917	-0.03	0.0305	-18.9876	39.6253	-2.6822
10	9.7765	11.2765	5.8034	21.3895	29.4238	65.077	-0.0679	0.2092	0.421	0.7969	-0.9679	0.4075	-0.3955	-1.6901	1.0358	-0.046	-0.1084	0.0279	0.3539	-0.1275	0.207	-12.5171	43.0797	12.3818
11	27.1776	5.1203	8.2846	28.7279	11.3744	22.1755	-0.5271	0.9574	-0.1693	-1.7254	0.1548	0.7702	-0.2933	-0.9601	0.3723	-0.055	-0.0593	-0.0074	0.3627	-0.036	0.014	-4.8027	37.1759	-11.8081
12	16.5052	2.4857	1.4007	0.9164	2.0152	6.1248	-0.3034	0.2232	-0.3288	-0.2211	0.0391	-0.2263	0.3068	-0.0784	0.2643	-0.0404	-0.1169	0.0073	0.2316	-0.0815	0.009	-21.1325	34.53	-15.5378
13	14.7422	3.1263	-1.6547	2.1296	2.4698	5.6104	-0.2014	-0.2756	-0.0649	0.248	0.0319	-0.0687	0.0953	0.1081	0.1696	-0.0947	0.0792	-0.0088	0.2196	0.0321	0.1595	3.5789	36.3798	-9.2853
14	30.4013	5.0108	-10.4355	5.5641	-6.4684	8.3406	0.7027	1.7825	1.0684	1.0025	-0.0598	-0.114	1.8626	-1.1054	-0.6429	-0.3455	0.183	-0.0208	0.3922	-0.0588	0.2529	1.4094	34.55	-14.7111
15	11.9485	-1.1765	-1.7475	5.4162	7.7953	11.2199	0.6958	0.8434	0.9646	-1.9247	-0.9794	-0.2748	-1.2354	-0.2873	0.2836	0.1275	-0.1163	0.0905	0.521	-0.1205	0.0578	-10.81	42.9485	-13.4175
16	10.6577	4.0091	3.5523	16.7947	5.6141	3.1995	-0.1178	0.7088	0.5505	-0.26	-0.0141	-1.2405	0.413	0.2006	0.1319	-0.2097	0.0518	-0.0229	0.4346	0.0384	0.2597	2.7982	41.2641	-14.6433
17	28.768	-16.1228	-1.0645	56.5878	31.8319	69.8092	-0.8079	-0.3995	-0.3178	2.1204	1.9415	-1.3029	4.3256	2.9108	-1.1336	0.0777	0.1434	0.0195	0.5717	-0.06	0.1223	2.3138	35.6002	-18.389
18	12.4862	1.6699	1.7399	8.1248	-0.5313	5.1188	-0.1092	0.3573	0.3969	0.3556	-0.2444	-0.7652	-0.1589	0.1571	0.3536	-0.041	0.0596	-0.0101	0.3414	0.1022	0.2102	11.8154	41.9913	-13.3196
19	13.5671	8.0026	7.6171	18.7352	12.9063	17.0488	0.3395	0.0129	0.1464	0.4991	-0.2466	-0.3072	0.5528	-0.5227	-0.0929	-0.1031	0.026	-0.0048	0.2809	-0.0365	0.0641	-4.1804	37.5508	-12.4178

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	0 - 4	2 - 6
2	X-RAY DIFFRACTION	2	A	A	5 - 10	7 - 12
3	X-RAY DIFFRACTION	3	A	A	11 - 17	13 - 19
4	X-RAY DIFFRACTION	4	A	A	18 - 25	20 - 27
5	X-RAY DIFFRACTION	5	A	A	26 - 35	28 - 37
6	X-RAY DIFFRACTION	6	A	A	36 - 47	38 - 49
7	X-RAY DIFFRACTION	7	A	A	48 - 56	50 - 58
8	X-RAY DIFFRACTION	8	A	A	57 - 63	59 - 65
9	X-RAY DIFFRACTION	9	A	A	64 - 71	66 - 73
10	X-RAY DIFFRACTION	10	A	A	72 - 76	74 - 78
11	X-RAY DIFFRACTION	11	B	B	0 - 5	2 - 7
12	X-RAY DIFFRACTION	12	B	B	6 - 13	8 - 15
13	X-RAY DIFFRACTION	13	B	B	14 - 25	16 - 27
14	X-RAY DIFFRACTION	14	B	B	26 - 32	28 - 34
15	X-RAY DIFFRACTION	15	B	B	33 - 38	35 - 40
16	X-RAY DIFFRACTION	16	B	B	39 - 47	41 - 49
17	X-RAY DIFFRACTION	17	B	B	48 - 52	50 - 54
18	X-RAY DIFFRACTION	18	B	B	53 - 63	55 - 65
19	X-RAY DIFFRACTION	19	B	B	64 - 72	66 - 74

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