PDB-3eae: PWWP domain of human hepatoma-derived growth factor 2 (HDGF2)

ID or keywords:

Entry

Database: PDB / ID: 3eae

Title

PWWP domain of human hepatoma-derived growth factor 2 (HDGF2)

Components

Hepatoma-derived growth factor-related protein 2

Keywords

SIGNALING PROTEIN / human hepatoma-derived growth factor 2 / hepatoma-derived growth factor-related protein 2 / HDGF2 / Structural Genomics / Structural Genomics Consortium / SGC / Phosphoprotein

Function / homology

Function and homology information

H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / DNA repair-dependent chromatin remodeling / muscle organ development / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / positive regulation of cell growth ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.24 Å

Authors

Amaya, M.F. / Zeng, H. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)

Citation

Journal: Plos One / Year: 2011
Title: Structural and Histone Binding Ability Characterizations of Human PWWP Domains.
Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Amaya, M.F. / Xu, C. / Dombrovski, L. / Qiu, W. / Wang, Y. / Min, J.

History

Deposition	Aug 25, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jul 20, 2011	Group: Database references
Revision 1.3	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.4	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3eae.cif.gz	48.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3eae_validation.pdf.gz	425.7 KB	Display	wwPDB validaton report
Full document	3eae_full_validation.pdf.gz	427.5 KB	Display
Data in XML	3eae_validation.xml.gz	8.4 KB	Display
Data in CIF	3eae_validation.cif.gz	10.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ea/3eae ftp://data.pdbj.org/pub/pdb/validation_reports/ea/3eae	HTTPS FTP

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Related structure data

Related structure data	3l42C 3llrC 3lyiC 3mo8C 3pfsC 3pmiC 3qbyC 3qj6C 3qkjC 2htsS 2nluS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fbk-d 3on1-d 2kky-d 4mmj-d 5dom-d 6ue6-6 1gq5-d 2mzt-d 3kz5-2 3fc7-1 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	#139 - Jul 2011 DNA Methyltransferase similarity (4)

Deposited unit

A: Hepatoma-derived growth factor-related protein 2

B: Hepatoma-derived growth factor-related protein 2

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

1

A: Hepatoma-derived growth factor-related protein 2

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

2

B: Hepatoma-derived growth factor-related protein 2

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

Unit cell

Length a, b, c (Å)	41.555, 59.950, 104.942
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Hepatoma-derived growth factor-related protein 2 / HRP-2 / Hepatoma-derived growth factor 2 Mass: 10657.184 Da / Num. of mol.: 2 / Fragment: residues 1-93 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFRP2, HDGF2, UNQ785/PRO1604 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z4V5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Hepatoma-derived growth factor-related protein 2 / HRP-2 / Hepatoma-derived growth factor 2

Mass: 10657.184 Da / Num. of mol.: 2 / Fragment: residues 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: HDGFRP2, HDGF2, UNQ785/PRO1604 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q7Z4V5

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.07 Å³/Da / Density % sol: 59.89 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2.0 M NH4SO4, 0.2 M K/Na tart, 0.1 M Na Citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 200 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.24→40 Å / Num. obs: 12780 / % possible obs: 99.7 % / Redundancy: 6.9 % / R_merge(I) obs: 0.084 / Χ²: 1.261 / Net I/σ(I): 19.947

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.3-2.34	6.4	0.647	600	1.527	1	98.5
2.34-2.38	6.6	0.635	587	1.457	1	99.8
2.38-2.43	6.8	0.55	599	1.353	1	99
2.43-2.48	7.1	0.478	607	1.425	1	99.7
2.48-2.53	7.1	0.435	619	1.421	1	100
2.53-2.59	7.2	0.35	610	1.448	1	100
2.59-2.66	7.2	0.318	603	1.472	1	100
2.66-2.73	7.2	0.268	617	1.434	1	100
2.73-2.81	7.2	0.206	606	1.507	1	100
2.81-2.9	7.2	0.181	621	1.624	1	100
2.9-3	7.1	0.146	615	1.726	1	100
3-3.12	7.2	0.124	609	1.162	1	100
3.12-3.26	7.1	0.108	612	1.124	1	100
3.26-3.44	7.1	0.09	630	1.052	1	100
3.44-3.65	7	0.081	616	1.093	1	100
3.65-3.93	7	0.08	630	1.181	1	100
3.93-4.33	6.9	0.074	639	1.042	1	100
4.33-4.95	6.8	0.061	634	0.883	1	100
4.95-6.24	6.5	0.046	651	0.622	1	100
6.24-40	6.2	0.047	694	0.668	1	97.1

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB Entries 2HTS and 2NLU

2hts

2nlu

Resolution: 2.24→40 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.923 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.564 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26	632	4.9 %	RANDOM
R_work	0.224	-	-	-
obs	0.225	12780	96.39 %	-

Solvent computation

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

Displacement parameters

B_iso max: 72.61 Å² / B_iso mean: 30.079 Å² / B_iso min: 10.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.26 Å²	0 Å²	0 Å²
2-	-	3.56 Å²	0 Å²
3-	-	-	-2.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.24→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1322	0	0	45	1367

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1379
X-RAY DIFFRACTION	r_angle_refined_deg	1.261	1.934	1878
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.081	5	164
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.567	23.623	69
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.386	15	177
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.709	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	173
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1134
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	486
X-RAY DIFFRACTION	r_nbtor_refined	0.318	0.2	893
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	37
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.148	0.2	16
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.188	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.605	1.5	850
X-RAY DIFFRACTION	r_mcangle_it	1.009	2	1329
X-RAY DIFFRACTION	r_scbond_it	1.68	3	615
X-RAY DIFFRACTION	r_scangle_it	2.379	4.5	549

LS refinement shell

Resolution: 2.236→2.293 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.363	37	-
R_work	0.293	724	-
all	-	761	-
obs	-	-	79.94 %

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	16.428	-5.6157	7.1118	8.0876	-4.9561	12.8956	-0.2616	0.8433	0.9443	0.1628	0.0291	-0.4283	-0.6381	0.1133	0.2326	0.0517	-0.0684	0.0233	0.1942	0.0606	0.1874	26.0601	48.8531	-5.0603
2	6.1298	-0.8441	-2.1573	4.9149	-2.2751	6.1488	-0.029	0.2625	-0.7442	0.1125	0.0555	0.3212	0.7963	-0.3814	-0.0264	0.1202	-0.1112	-0.0041	0.1959	-0.006	0.1869	22.0981	36.0774	2.4575
3	12.6104	4.6747	3.802	2.4123	-1.5577	14.1055	0.1076	2.1868	-1.3004	-0.4893	0.2422	-0.8771	-0.2167	1.1787	-0.3498	0.3776	0.0646	0.1391	0.634	-0.2338	0.2771	28.3795	37.3522	-14.6102
4	4.9573	-1.1832	4.9798	5.3115	-3.694	22.0441	0.0855	0.4758	-0.1974	-0.1805	-0.1021	0.0791	0.2607	-0.4642	0.0166	0.0604	-0.0517	0.0002	0.1361	-0.0416	0.1395	24.8636	36.8654	-5.2275
5	8.2173	-4.2233	0.6276	5.5034	0.7077	4.8835	-0.1443	0.3407	-0.4028	-0.1715	0.1736	0.1934	0.3721	-0.2485	-0.0293	0.0446	-0.0727	0.0376	0.1919	0.01	0.1017	22.3375	39.1224	-1.6845
6	7.8081	-4.1345	5.3805	13.9963	-6.6826	16.6427	-0.386	-0.9478	0.0176	0.7793	0.1417	0.4107	-0.2294	-0.9472	0.2442	0.0133	0.082	0.0454	0.2777	0.0062	0.1316	22.0366	41.6557	11.7228
7	9.9495	-4.3402	9.9848	4.572	-2.4624	11.3583	0.0195	0.5934	-1.1328	-0.2669	0.5606	-0.0515	1.2946	-0.5565	-0.5801	0.2994	-0.093	0.0323	0.1529	0.0627	0.2605	26.7631	30.189	9.8295
8	10.5581	3.001	-5.6948	1.8267	-2.6427	16.1106	-0.1621	-0.2947	-0.5481	-0.0752	-0.1218	-0.2997	0.2668	0.8832	0.284	0.0858	0.0213	0.0129	0.2057	0.0455	0.1817	35.5677	38.3975	4.5513
9	24.9467	-4.1764	3.1747	18.0888	-10.5505	14.9676	0.2494	-1.911	1.1378	2.323	-0.6121	-1.4048	-2.4148	1.4887	0.3627	0.646	-0.2187	-0.1473	0.5593	0.0179	0.1607	42.3637	42.6148	30.4898
10	9.8076	-6.2237	4.9084	12.1116	3.3085	15.4641	0.6355	-1.0611	-1.5858	-0.0906	-0.2916	0.2451	1.3742	0.9112	-0.3439	0.2127	0.0726	-0.0567	0.332	0.2431	0.3991	44.0359	29.0829	23.0252
11	6.3231	8.0843	3.8921	11.5535	-0.1551	24.0216	-0.2294	-1.0918	-0.8569	0.3923	-0.2724	0.394	0.0846	0.0172	0.5017	0.1868	0.0108	-0.1231	0.1512	0.1637	-0.0312	38.079	35.5639	26.9757
12	15.5654	2.7396	9.4699	4.5238	-0.6061	22.2879	0.5823	-1.0634	0.2433	0.6815	-0.648	-0.377	-0.0129	-0.2531	0.0657	0.2196	-0.0469	-0.0484	0.2665	0.2041	0.1096	37.5517	33.9404	30.3959
13	28.0052	5.6948	-2.2335	7.5452	-7.9716	15.6982	0.8896	-1.8175	-1.2009	1.0767	-1.1633	-0.4973	-0.0507	2.5198	0.2737	0.1525	0.0003	-0.0799	0.2926	0.0889	0.0392	44.3378	33.7639	28.7247
14	19.0965	4.0313	-5.3002	30.146	0.5626	36.815	0.4131	1.1412	0.6484	-0.3665	-0.8767	-0.0085	-1.1489	2.0986	0.4636	-0.0142	-0.0125	-0.0228	0.3763	0.1985	0.0701	46.2061	39.5062	16.6555
15	4.844	8.5262	-3.4833	37.8123	6.6617	12.5919	-0.508	1.1011	-1.8543	-0.7518	0.105	-1.3061	2.0672	1.1434	0.4029	0.1564	0.2424	-0.1207	0.2204	0.0551	0.1927	37.9973	29.2374	14.235
16	3.7185	2.8189	3.8104	7.5554	-3.8962	13.7175	0.1656	-0.5523	-0.0775	0.4448	-0.1226	0.6245	-0.65	-0.4737	-0.043	0.1011	0.0096	0.0645	0.2613	0.0882	0.1328	32.3453	38.3147	20.1254

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	2 - 10	2 - 10
2	X-RAY DIFFRACTION	2	A	A	11 - 25	11 - 25
3	X-RAY DIFFRACTION	3	A	A	26 - 36	26 - 36
4	X-RAY DIFFRACTION	4	A	A	37 - 47	37 - 47
5	X-RAY DIFFRACTION	5	A	A	48 - 62	48 - 62
6	X-RAY DIFFRACTION	6	A	A	63 - 72	63 - 72
7	X-RAY DIFFRACTION	7	A	A	73 - 79	73 - 79
8	X-RAY DIFFRACTION	8	A	A	80 - 93	80 - 93
9	X-RAY DIFFRACTION	9	B	B	5 - 10	5 - 10
10	X-RAY DIFFRACTION	10	B	B	11 - 20	11 - 20
11	X-RAY DIFFRACTION	11	B	B	21 - 26	21 - 26
12	X-RAY DIFFRACTION	12	B	B	27 - 48	27 - 48
13	X-RAY DIFFRACTION	13	B	B	49 - 61	49 - 61
14	X-RAY DIFFRACTION	14	B	B	62 - 68	62 - 68
15	X-RAY DIFFRACTION	15	B	B	69 - 76	69 - 76
16	X-RAY DIFFRACTION	16	B	B	77 - 90	77 - 90

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