PDB-2xp0: C-terminal cysteine-rich domain of human CHFR

ID or keywords:

Entry

Database: PDB / ID: 2xp0

Title

C-terminal cysteine-rich domain of human CHFR

Components

E3 UBIQUITIN-PROTEIN LIGASE CHFR

Keywords

LIGASE / ZINC-BINDING / PBZ / MITOSIS / ANTEPHASE CHECKPOINT

Function / homology

Function and homology information

meiotic spindle checkpoint signaling / mitotic G2/M transition checkpoint / positive regulation of protein ubiquitination / protein destabilization / RING-type E3 ubiquitin transferase / PML body / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.978 Å

Authors

Oberoi, J. / Bayliss, R.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Structural Basis of Poly(Adp-Ribose) Recognition by the Multizinc Binding Domain of Checkpoint with Forkhead-Associated and Ring Domains (Chfr).
Authors: Oberoi, J. / Richards, M.W. / Crumpler, S. / Brown, N. / Blagg, J. / Bayliss, R.

History

Deposition	Aug 24, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 29, 2010	Provider: repository / Type: Initial release
Revision 1.1	Sep 5, 2012	Group: Derived calculations / Version format compliance
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xp0.cif.gz	196.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2xp0.ent.gz	156.3 KB	Display	PDB format
PDBx/mmJSON format	2xp0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2xp0_validation.pdf.gz	431.8 KB	Display	wwPDB validaton report
Full document	2xp0_full_validation.pdf.gz	432.2 KB	Display
Data in XML	2xp0_validation.xml.gz	23.1 KB	Display
Data in CIF	2xp0_validation.cif.gz	35.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xp/2xp0 ftp://data.pdbj.org/pub/pdb/validation_reports/xp/2xp0	HTTPS FTP

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Related structure data

Related structure data	2xocSC 2xoyC 2xozC 1lgp 1lgq C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2xoy-1 2xoc-1 2xoc-2 2xoy-2 2xoz-1 5e80-d 2xoz-2 1m9x-2 5f2u-d 4az9-1 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	#122 - Feb 2010 Enhanceosome similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (2) #163 - Jul 2013 HIV Capsid similarity (2) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: E3 UBIQUITIN-PROTEIN LIGASE CHFR

B: E3 UBIQUITIN-PROTEIN LIGASE CHFR

hetero molecules

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

1

A: E3 UBIQUITIN-PROTEIN LIGASE CHFR

hetero molecules

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

2

B: E3 UBIQUITIN-PROTEIN LIGASE CHFR

hetero molecules

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

Unit cell

Length a, b, c (Å)	163.010, 52.030, 82.520
Angle α, β, γ (deg.)	90.00, 105.73, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	E3 UBIQUITIN-PROTEIN LIGASE CHFR / CHECKPOINT WITH FORKHEAD AND RING FINGER DOMAINS PROTEIN / RING FINGER PROTEIN 196 / CHFR Mass: 30736.721 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH REGION, RESIDUES 394-664 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL References: UniProt: Q96EP1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.66 % / Description: NONE
Crystal grow	Details: 12% PEG 20000, 0.1M MES PH 6.5, 0.1M KCL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.98→49.51 Å / Num. obs: 46604 / % possible obs: 99.5 % / Observed criterion σ(I): 6 / Redundancy: 3.5 % / B_iso Wilson estimate: 18.91 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 9.1
Reflection shell	Resolution: 1.98→2.09 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOC

2xoc

Resolution: 1.978→39.715 Å / SU ML: 0.23 / σ(F): 0.01 / Phase error: 18.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.202	3878	8.6 %
R_work	0.1607	-	-
obs	0.1642	45210	96.42 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.619 Å² / k_sol: 0.326 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.5658 Å²	0 Å²	0.2431 Å²
2-	-	3.7974 Å²	-0 Å²
3-	-	-	0.7684 Å²

Refinement step

Cycle: LAST / Resolution: 1.978→39.715 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3386	0	10	591	3987

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3497
X-RAY DIFFRACTION	f_angle_d	1.028	4751
X-RAY DIFFRACTION	f_dihedral_angle_d	18.159	1286
X-RAY DIFFRACTION	f_chiral_restr	0.074	504
X-RAY DIFFRACTION	f_plane_restr	0.005	627

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.978-2.0022	0.2641	146	0.2227	1368	X-RAY DIFFRACTION	90
2.0022-2.0275	0.2655	120	0.2099	1384	X-RAY DIFFRACTION	92
2.0275-2.0542	0.2672	127	0.2076	1438	X-RAY DIFFRACTION	94
2.0542-2.0823	0.2097	126	0.2034	1447	X-RAY DIFFRACTION	93
2.0823-2.1121	0.2366	122	0.1996	1388	X-RAY DIFFRACTION	93
2.1121-2.1436	0.2329	121	0.1863	1454	X-RAY DIFFRACTION	94
2.1436-2.1771	0.2361	124	0.1821	1490	X-RAY DIFFRACTION	95
2.1771-2.2128	0.2591	113	0.1776	1440	X-RAY DIFFRACTION	96
2.2128-2.2509	0.2263	146	0.165	1429	X-RAY DIFFRACTION	95
2.2509-2.2918	0.2038	141	0.1539	1473	X-RAY DIFFRACTION	96
2.2918-2.3359	0.1884	144	0.1517	1429	X-RAY DIFFRACTION	96
2.3359-2.3836	0.1911	147	0.1532	1486	X-RAY DIFFRACTION	97
2.3836-2.4354	0.2238	139	0.1546	1466	X-RAY DIFFRACTION	97
2.4354-2.4921	0.2031	157	0.1586	1455	X-RAY DIFFRACTION	97
2.4921-2.5544	0.176	147	0.1543	1448	X-RAY DIFFRACTION	96
2.5544-2.6234	0.2102	133	0.1538	1493	X-RAY DIFFRACTION	97
2.6234-2.7006	0.1854	144	0.155	1500	X-RAY DIFFRACTION	98
2.7006-2.7877	0.2197	141	0.158	1485	X-RAY DIFFRACTION	98
2.7877-2.8874	0.2128	135	0.1684	1490	X-RAY DIFFRACTION	97
2.8874-3.0029	0.2065	144	0.168	1496	X-RAY DIFFRACTION	99
3.0029-3.1395	0.2351	143	0.1689	1513	X-RAY DIFFRACTION	99
3.1395-3.305	0.2379	143	0.1634	1536	X-RAY DIFFRACTION	99
3.305-3.5119	0.1763	144	0.1525	1519	X-RAY DIFFRACTION	99
3.5119-3.7829	0.169	144	0.1335	1510	X-RAY DIFFRACTION	99
3.7829-4.1632	0.16	145	0.128	1518	X-RAY DIFFRACTION	99
4.1632-4.7648	0.162	145	0.1213	1554	X-RAY DIFFRACTION	99
4.7648-5.9998	0.1433	147	0.1361	1530	X-RAY DIFFRACTION	98
5.9998-39.7227	0.192	150	0.1559	1593	X-RAY DIFFRACTION	99

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	1.4505	0.1172	0.1871	0.471	-0.122	2.319	0.4737	-0.064	0.1683	-0.0816	0.0296	0.0682	0.1543	-0.3411	-0.3081	0.2199	0.0214	0.0857	0.2892	0.0187	0.1998	27.8199	24.1048	52.1836
2	0.0336	-0.1788	-0.0598	1.6252	0.3076	0.3474	0.0895	0.2281	-0.1058	0.0889	-0.2734	0.4216	0.0016	-0.39	0.1194	0.0887	0.0971	0.025	0.1929	0.0321	0.1741	34.412	27.4838	38.955
3	0.1309	-0.0273	-0.1083	0.2034	0.1979	0.2617	-0.0545	-0.0914	-0.0047	0.0555	0.0701	0.0004	-0.0776	-0.0391	-0.012	0.0952	0.0443	0.0035	0.1549	0.0245	0.0634	45.8568	25.4196	37.0581
4	0.3676	0.0029	0.0463	0.6087	-0.1059	0.324	0.0201	-0.0191	0.0113	0.1193	0.0322	0.0094	0.0532	-0.0549	-0.0526	0.0537	-0.0096	-0.0223	0.0654	0.022	0.0466	65.1505	9.946	28.7204
5	2.0441	0.3451	0.0012	0.0625	0.047	0.7331	-0.1491	0.0064	0.391	0.0056	0.181	-0.0158	-0.2296	0.141	-0.0168	0.1436	-0.021	-0.0143	0.0512	-0.0203	0.1061	63.2016	25.4891	23.7008
6	0.4062	0.0059	-0.2281	0.2058	0.0505	0.8862	0.0096	0.0328	-0.0491	-0.0303	0.0603	0.0124	-0.1168	-0.1067	-0.0808	0.0653	0.0114	-0.0183	0.0529	0.0295	0.0622	54.2932	20.9985	24.409
7	0.4623	0.2602	0.522	0.5239	0.5217	0.9033	0.058	0.0705	-0.1795	-0.0184	0.0893	-0.1462	0.0771	0.1188	-0.1416	0.0318	-0.0012	-0.0298	0.0133	-0.0107	0.0562	64.9049	3.802	16.4737
8	1.8176	-0.6334	-0.3271	0.5937	0.7722	1.2353	0.191	0.4464	0.1687	0.0025	-0.1991	-0.1142	-0.0756	-0.1374	0.0158	-0.0003	0.0217	-0.2604	0.1056	0.0935	-0.3981	58.5579	8.2303	4.2278
9	1.0124	-0.2781	0.7074	1.0208	-0.0168	1.2469	-0.234	0.0899	0.1317	0.1567	0.0943	-0.1322	0.091	-0.394	0.1405	0.0846	-0.0504	0.0163	0.1659	-0.053	0.0851	6.9604	-11.5113	32.1238
10	0.5997	0.129	-0.1499	0.463	0.1203	0.2489	-0.0671	0.2017	-0.0796	-0.0538	0.0299	-0.0022	0.0095	-0.1085	0.0245	0.0525	-0.0463	0.02	0.216	-0.0134	0.0577	12.172	-13.6839	17.4044
11	0.7332	-0.1769	-0.1153	0.1567	0.0842	0.1665	0.048	-0.1293	0.0853	0.0437	-0.0539	-0.0338	0.0531	-0.0315	0.0038	0.0688	-0.0331	0.017	0.0722	-0.0057	0.053	31.6392	-10.0244	15.8309
12	0.5461	0.0802	0.1407	0.0561	-0.0336	0.2082	0.0312	-0.0138	0.0567	-0.0049	-0.0278	-0.0272	0.001	-0.0081	-0.0066	0.0292	-0.0136	0.0048	0.0066	0.0069	0.0258	40.9634	-7.6538	4.225
13	0.3868	0.0558	0.0516	0.1455	0.2526	0.5759	0.0927	-0.0126	-0.1621	0.0974	0.0748	-0.286	0.1195	0.0426	-0.1999	0.1264	-0.0058	-0.0339	0.0353	0.0147	0.1815	57.1755	-19.0384	7.9728
14	0.3846	-0.6948	-0.1382	1.2807	0.2669	0.0474	0.1218	-0.031	-0.1204	-0.2688	-0.074	0.2357	0.1014	0.1716	-0.0419	0.1221	0.0392	-0.0139	0.0685	-0.0263	0.0957	54.0478	-24.2398	0.2886

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 425:477)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 478:500)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 501:543)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 544:571)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 572:588)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 589:617)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 618:657)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 658:663)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 425:476)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 477:507)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 508:557)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 558:630)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 631:655)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 656:663)

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