PDB-3pmi: PWWP Domain of Human Mutated Melanoma-Associated Antigen 1

ID or keywords:

Entry

Database: PDB / ID: 3pmi

Title

PWWP Domain of Human Mutated Melanoma-Associated Antigen 1

Components

PWWP domain-containing protein MUM1

Keywords

PROTEIN BINDING / Structural Genomics Consortium / SGC / nucleus

Function / homology

Function and homology information

nucleosome binding / chromatin organization / DNA repair / nucleoplasm / nucleus / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.82 Å

Authors

Lam, R. / Zeng, H. / Loppnau, P. / 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	Nov 17, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 15, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Mar 28, 2012	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pmi.cif.gz	208.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3pmi.ent.gz	168.5 KB	Display	PDB format
PDBx/mmJSON format	3pmi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3pmi_validation.pdf.gz	472.3 KB	Display	wwPDB validaton report
Full document	3pmi_full_validation.pdf.gz	479.9 KB	Display
Data in XML	3pmi_validation.xml.gz	21.4 KB	Display
Data in CIF	3pmi_validation.cif.gz	27.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pm/3pmi ftp://data.pdbj.org/pub/pdb/validation_reports/pm/3pmi	HTTPS FTP

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Related structure data

Related structure data	3eaeC 3l42C 3llrC 3lyiC 3mo8C 3pfsC 3qbyC 3qj6C 3qkjC C: citing same article (ref.)
Similar structure data	5w9q-2 6fdl-1 3qmg-d 2xeu-1 2kt0-d 2i9c-d 5rtt-2 5rta-2 4kk3-d 1l4y-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: PWWP domain-containing protein MUM1

B: PWWP domain-containing protein MUM1

C: PWWP domain-containing protein MUM1

D: PWWP domain-containing protein MUM1

hetero molecules

63 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PWWP domain-containing protein MUM1

hetero molecules

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

2

B: PWWP domain-containing protein MUM1

hetero molecules

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

3

C: PWWP domain-containing protein MUM1

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

4

D: PWWP domain-containing protein MUM1

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

5

B: PWWP domain-containing protein MUM1

hetero molecules

A: PWWP domain-containing protein MUM1

C: PWWP domain-containing protein MUM1

D: PWWP domain-containing protein MUM1

hetero molecules

defined by software
63 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.044, 57.716, 187.072
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	GLN	GLN	3	C	C	482 - 484	77 - 79
2	1	PHE	PHE	GLN	GLN	3	B	B	482 - 484	77 - 79
1	2	LYS	LYS	PRO	PRO	3	B	B	419 - 424	14 - 19
2	2	LYS	LYS	PRO	PRO	3	A	A	419 - 424	14 - 19
1	3	LEU	LEU	TRP	TRP	3	D	D	415 - 417	10 - 12
2	3	LEU	LEU	TRP	TRP	3	C	C	415 - 417	10 - 12
1	4	ARG	ARG	LYS	LYS	4	C	C	434 - 439	29 - 34
2	4	ARG	ARG	LYS	LYS	4	A	A	434 - 439	29 - 34
1	5	LYS	LYS	PHE	PHE	3	D	D	464 - 466	59 - 61
2	5	LYS	LYS	PHE	PHE	3	B	B	464 - 466	59 - 61
1	6	GLN	GLN	GLN	GLN	3	C	C	435	30
2	6	GLN	GLN	GLN	GLN	3	A	A	435	30
1	7	ILE	ILE	ILE	ILE	3	A	A	525	120
2	7	ILE	ILE	ILE	ILE	3	C	C	525	120
1	8	VAL	VAL	LEU	LEU	3	A	A	529 - 530	124 - 125
2	8	VAL	VAL	LEU	LEU	3	B	B	529 - 530	124 - 125
1	9	PHE	PHE	GLU	GLU	2	D	D	410 - 411	5 - 6
2	9	PHE	PHE	GLU	GLU	2	C	C	410 - 411	5 - 6
1	10	GLN	GLN	ASP	ASP	4	B	B	435 - 437	30 - 32
2	10	GLN	GLN	ASP	ASP	4	D	D	435 - 437	30 - 32

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	PWWP domain-containing protein MUM1 / Mutated melanoma-associated antigen 1 / MUM-1 / Protein expandere Mass: 15681.721 Da / Num. of mol.: 4 / Fragment: PWWP Domain (UNP residues 405-538) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EXPAND1, MUM1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q2TAK8
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 2 / Source method: obtained synthetically
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.07 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG3350, 0.1M Ammonium Sulfate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97931 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2010
Details: Rosenbaum-Rock high-resolution double-crystal monochromator

Radiation

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

Radiation wavelength

Wavelength: 0.97931 Å / Relative weight: 1

Reflection

Resolution: 2.85→50 Å / Num. obs: 14914 / % possible obs: 99.9 % / Redundancy: 6.8 % / R_merge(I) obs: 0.11 / Χ²: 1.228 / Net I/σ(I): 10.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.85-2.95	7.1	0.522	1455	0.85	1	100
2.95-3.07	7.1	0.367	1476	0.913	1	100
3.07-3.21	7.1	0.247	1447	0.982	1	100
3.21-3.38	7	0.169	1448	1.097	1	100
3.38-3.59	7	0.127	1473	1.068	1	100
3.59-3.87	6.9	0.102	1477	1.112	1	100
3.87-4.26	6.8	0.087	1494	1.164	1	100
4.26-4.87	6.6	0.091	1489	1.243	1	100
4.87-6.14	6.6	0.094	1535	1.571	1	99.9
6.14-50	6.1	0.085	1620	2.353	1	99.4

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.82 Å / D res low: 47.44 Å / FOM : 0.407 / FOM acentric: 0.453 / FOM centric: 0.156 / Reflection: 14865 / Reflection acentric: 12545 / Reflection centric: 2314

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8.65-10.51	0.4	0.546	0.097	251	168	81
7.52-8.65	0.524	0.65	0.18	286	209	77
6.75-7.52	0.546	0.654	0.206	319	242	77
6.17-6.75	0.532	0.629	0.216	351	269	82
5.72-6.17	0.549	0.643	0.196	384	303	81
5.35-5.72	0.512	0.593	0.189	401	321	80
5.05-5.35	0.527	0.608	0.153	430	354	76
4.79-5.05	0.473	0.54	0.163	451	370	81
4.57-4.79	0.475	0.548	0.145	462	379	82
4.38-4.57	0.446	0.505	0.148	501	418	83
4.21-4.38	0.449	0.514	0.111	495	415	80
4.06-4.21	0.453	0.514	0.119	541	457	84
3.92-4.06	0.465	0.515	0.159	542	466	76
3.8-3.92	0.447	0.497	0.164	559	474	85
3.68-3.8	0.439	0.485	0.125	579	506	73
3.58-3.68	0.408	0.46	0.114	599	509	90
3.49-3.58	0.439	0.485	0.115	601	526	75
3.4-3.49	0.399	0.439	0.125	624	545	79
3.32-3.4	0.379	0.413	0.172	649	558	90
3.24-3.32	0.378	0.406	0.148	633	564	69
3.17-3.24	0.348	0.384	0.118	695	600	95
3.1-3.17	0.346	0.366	0.189	669	593	76
3.04-3.1	0.339	0.362	0.164	683	605	78
2.98-3.04	0.314	0.331	0.188	726	641	85
2.93-2.98	0.301	0.315	0.184	713	636	77
2.87-2.93	0.296	0.311	0.181	740	654	85
2.82-2.87	0.269	0.281	0.164	641	573	68

Phasing dm

FOM : 0.71 / FOM acentric: 0.72 / FOM centric: 0.63 / Reflection: 14866 / Reflection acentric: 12552 / Reflection centric: 2314

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5-8.1	0.86	0.9	0.7	2056	1613	443
4-5	0.87	0.89	0.74	2527	2106	421
3.5-4	0.8	0.82	0.67	2520	2166	354
3-3.5	0.63	0.65	0.52	4414	3871	543
2.8-3	0.42	0.43	0.31	2635	2344	291

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
RESOLVE	2.15	phasing
REFMAC	refmac_5.6.0081	refinement
PDB_EXTRACT	3.1	data extraction
EPICS-based	beamline control	data collection
data	acquisition systems	data collection
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.82→50 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.873 / WR_factor R_free: 0.306 / WR_factor R_work: 0.229 / Occupancy max: 1 / Occupancy min: 1 / SU B: 40.114 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3039	751	5.1 %	RANDOM
R_work	0.2278	-	-	-
obs	0.2315	14861	99.15 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 79.7 Å² / B_iso mean: 55.342 Å² / B_iso min: 2.67 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0 Å²	0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	0.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.82→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3797	0	41	0	3838

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	3935
X-RAY DIFFRACTION	r_angle_refined_deg	1.289	1.938	5331
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.929	5	481
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.927	23.237	173
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.382	15	623
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.495	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	575
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	2985

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	C	12	TIGHT POSITIONAL	0.04	0.05
1	C	12	LOOSE POSITIONAL	0.04	5
1	C	12	TIGHT THERMAL	4.75	0.5
1	C	12	LOOSE THERMAL	4.66	10
2	B	24	TIGHT POSITIONAL	0.02	0.05
2	B	15	LOOSE POSITIONAL	0.02	5
2	B	24	TIGHT THERMAL	2.32	0.5
2	B	15	LOOSE THERMAL	3.42	10
3	D	12	TIGHT POSITIONAL	0.02	0.05
3	D	17	LOOSE POSITIONAL	0.04	5
3	D	12	TIGHT THERMAL	4.22	0.5
3	D	17	LOOSE THERMAL	2.98	10
4	C	34	MEDIUM POSITIONAL	0.3	0.5
4	C	34	MEDIUM THERMAL	6.47	2
5	D	12	TIGHT POSITIONAL	0.02	0.05
5	D	18	LOOSE POSITIONAL	0.03	5
5	D	12	TIGHT THERMAL	1.16	0.5
5	D	18	LOOSE THERMAL	1.74	10
6	C	4	TIGHT POSITIONAL	0.04	0.05
6	C	1	LOOSE POSITIONAL	0.06	5
6	C	4	TIGHT THERMAL	4.81	0.5
6	C	1	LOOSE THERMAL	5.47	10
7	A	4	TIGHT POSITIONAL	0.04	0.05
7	A	4	LOOSE POSITIONAL	0.11	5
7	A	4	TIGHT THERMAL	1.04	0.5
7	A	4	LOOSE THERMAL	1.22	10
8	A	8	TIGHT POSITIONAL	0.02	0.05
8	A	7	LOOSE POSITIONAL	0.14	5
8	A	8	TIGHT THERMAL	7.51	0.5
8	A	7	LOOSE THERMAL	7.27	10
9	D	8	TIGHT POSITIONAL	0.02	0.05
9	D	2	MEDIUM POSITIONAL	0.04	0.5
9	D	8	TIGHT THERMAL	4.4	0.5
9	D	2	MEDIUM THERMAL	3.83	2
10	B	18	MEDIUM POSITIONAL	0.31	0.5
10	B	18	MEDIUM THERMAL	6.26	2

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.824-2.897	0.401	48	0.312	936	1101	89.373
2.897-2.977	0.34	58	0.26	974	1033	99.903
2.977-3.063	0.388	64	0.262	982	1047	99.904
3.063-3.156	0.351	53	0.25	916	969	100
3.156-3.259	0.331	51	0.227	938	989	100
3.259-3.373	0.273	43	0.225	894	937	100
3.373-3.5	0.343	36	0.223	863	899	100
3.5-3.642	0.336	43	0.214	844	887	100
3.642-3.803	0.281	38	0.189	793	831	100
3.803-3.988	0.359	41	0.219	777	818	100
3.988-4.202	0.286	43	0.214	728	771	100
4.202-4.455	0.262	40	0.197	695	735	100
4.455-4.76	0.252	36	0.187	647	683	100
4.76-5.137	0.248	36	0.191	608	645	99.845
5.137-5.622	0.266	30	0.213	574	604	100
5.622-6.275	0.276	22	0.236	531	553	100
6.275-7.227	0.264	26	0.262	477	503	100
7.227-8.806	0.29	21	0.22	399	420	100
8.806-12.264	0.295	10	0.235	328	338	100
12.264-50	0.495	12	0.398	206	226	96.46

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	4.358	0.654	-0.8714	1.093	1.413	5.7174	-0.0779	-0.0731	0.0131	0.1742	-0.0361	0.1085	0.3778	-0.3535	0.114	0.6495	0.0552	-0.0138	0.1376	-0.011	0.1134	40.616	13.047	134.584
2	3.865	-0.1007	0.2822	4.7647	1.016	3.9467	-0.1449	-0.1161	0.1854	0.132	-0.0306	0.4903	-0.3135	-0.3338	0.1755	0.4445	-0.0228	-0.0862	0.1295	0.0006	0.1528	49.51	0.069	154.817
3	2.2755	-0.1417	-0.7403	5.8775	0.3181	3.4134	-0.1564	-0.0661	-0.0634	-0.4636	0.2784	-0.0284	-0.4724	0.1815	-0.122	0.7829	-0.0063	0.0111	0.1789	-0.0657	0.0603	50.099	35.952	102.666
4	2.7513	1.0466	1.1604	7.9236	3.6895	5.973	0.0098	-0.1324	0.0743	0.5853	0.0081	0.2947	0.8795	-0.2589	-0.0179	0.6516	0.003	-0.0168	0.1344	0.0037	0.0446	30.552	5.903	111.066

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999
3	X-RAY DIFFRACTION	3	C	-10 - 9999
4	X-RAY DIFFRACTION	4	D	-10 - 9999

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Yorodumi