PDB-2uyy: Structure of the cytokine-like nuclear factor n-pac

ID or keywords:

Entry

Database: PDB / ID: 2uyy

Title

Structure of the cytokine-like nuclear factor n-pac

Components

N-PAC PROTEIN

Keywords

CYTOKINE / LONG-CHAIN DEHYDROGENASE

Function / homology

Function and homology information

: / chromatin-protein adaptor activity / Oxidoreductases / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription initiation-coupled chromatin remodeling / methylated histone binding / NAD binding / nucleosome / NADP binding ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Tickle, J. / Pilka, E.S. / Bunkoczi, G. / Berridge, G. / Smee, C. / Kavanagh, K.L. / Hozjan, V. / Niesen, F.H. / Papagrigoriou, E. / Pike, A.C.W. ...

Citation

Journal: To be Published
Title: The Structure of the Cytokine-Like Nuclear Factor N-Pac
Authors: Tickle, J. / Pilka, E.S. / Bunkoczi, G. / Berridge, G. / Smee, C. / Kavanagh, K.L. / Hozjan, V. / Niesen, F.H. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A. / Arrowsmith, C.H. / Edwards, ...

History

Deposition	Apr 20, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 3, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 24, 2018	Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3	Feb 28, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4	Dec 13, 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 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_asym_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_asym_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

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2uyy.cif.gz	236.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2uyy_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	2uyy_full_validation.pdf.gz	1.1 MB	Display
Data in XML	2uyy_validation.xml.gz	44.1 KB	Display
Data in CIF	2uyy_validation.cif.gz	62.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uy/2uyy ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uyy	HTTPS FTP

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Related structure data

Related structure data	1vpdS 2i9pS S: Starting model for refinement
Similar structure data	3pef-2 3pdu-2 3q3c-1 3obb-1 3pdu-1 3pef-1 4e21-1 1zpt-1 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	#127 - Jul 2010 Crystallins similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (4)

Deposited unit

A: N-PAC PROTEIN

B: N-PAC PROTEIN

C: N-PAC PROTEIN

D: N-PAC PROTEIN

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	134.180, 134.180, 261.463
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	262 - 304
2	1	1	2	B	262 - 304
3	1	1	2	C	262 - 304
4	1	1	2	D	262 - 304
1	2	1	5	A	305 - 309
2	2	1	5	B	305 - 309
3	2	1	5	C	305 - 309
4	2	1	5	D	305 - 309
1	3	1	2	A	310 - 352
2	3	1	2	B	310 - 352
3	3	1	2	C	310 - 352
4	3	1	2	D	310 - 352
1	4	1	5	A	353 - 355
2	4	1	5	B	353 - 355
3	4	1	5	C	353 - 355
4	4	1	5	D	353 - 355
1	5	1	2	A	356 - 553
2	5	1	2	B	356 - 553
3	5	1	2	C	356 - 553
4	5	1	2	D	356 - 553

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.32488, -0.91609, -0.235), (-0.91579, -0.36677, 0.16374), (-0.23619, 0.16202, -0.9581)	44.2988, 53.0766, 42.52633
2	given	(-0.96483, -0.00451, 0.26284), (-0.02791, -0.99244, -0.11951), (0.26139, -0.12265, 0.95741)	27.75931, 63.16761, 0.38689
3	given	(-0.96482, -0.00449, 0.26289), (-0.02796, -0.99243, -0.11957), (0.26144, -0.12271, 0.95739)	27.75884, 63.16805, 0.38797

#1: Protein	N-PAC PROTEIN / CYTOKINE-LIKE NUCLEAR FACTOR N-PAC Mass: 34086.984 Da / Num. of mol.: 4 / Fragment: RESIDUES 192-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q6P1Q2, UniProt: Q49A26*PLUS
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-NA7 / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE Mass: 623.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₅O₁₆P₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE FIRST 22 RESIDUES BELONG TO AN UNCLEAVED HIS6-TAG

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 61 %
Crystal grow	Details: 20% PEG3350 0.20 M KSCN

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9537
Detector	Type: MARRRESEARCH / Detector: CCD / Date: Mar 3, 2007
Radiation	Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.5→47.7 Å / Num. obs: 60779 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.61 % / R_merge(I) obs: 0.15 / Net I/σ(I): 8.93
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 4.42 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 2.35 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VPD, 2I9P

1vpd

2i9p

Resolution: 2.5→50 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.933 / SU B: 14.425 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.211	3072	5.1 %	RANDOM
R_work	0.17	-	-	-
obs	0.172	57621	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 29.62 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.84 Å²	0.92 Å²	0 Å²
2-	-	1.84 Å²	0 Å²
3-	-	-	-2.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8709	0	82	371	9162

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	8938
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	5868
X-RAY DIFFRACTION	r_angle_refined_deg	1.286	1.981	12110
X-RAY DIFFRACTION	r_angle_other_deg	0.885	3	14436
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.181	5	1163
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.664	25.182	357
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.025	15	1532
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.436	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1420
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9977
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1671
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	2072
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	6071
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	4575
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	4828
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	276
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.174	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.362	0.2	40
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.113	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.051	3	5766
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.978	5	9228
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	8.62	8	3202
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	11.457	11	2882
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1663	tight positional	0.04	0.05
2	B	1663	tight positional	0.03	0.05
3	C	1663	tight positional	0.04	0.05
4	D	1663	tight positional	0.04	0.05
1	A	1822	medium positional	0.35	0.5
2	B	1822	medium positional	0.39	0.5
3	C	1822	medium positional	0.34	0.5
4	D	1822	medium positional	0.46	0.5
1	A	65	loose positional	0.4	5
2	B	65	loose positional	0.95	5
3	C	65	loose positional	0.53	5
4	D	65	loose positional	0.55	5
1	A	1663	tight thermal	0.09	0.5
2	B	1663	tight thermal	0.1	0.5
3	C	1663	tight thermal	0.1	0.5
4	D	1663	tight thermal	0.1	0.5
1	A	1822	medium thermal	0.9	2
2	B	1822	medium thermal	0.85	2
3	C	1822	medium thermal	0.89	2
4	D	1822	medium thermal	0.9	2
1	A	65	loose thermal	3.5	10
2	B	65	loose thermal	3	10
3	C	65	loose thermal	3.8	10
4	D	65	loose thermal	3.55	10

LS refinement shell

Resolution: 2.5→2.56 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.443	225
R_work	0.383	4229

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	1.2754	-0.0698	-0.0161	1.2674	-0.4424	1.9409	0.0319	0.1076	0.0393	-0.1397	-0.084	-0.061	0.1268	0.0923	0.0521	0.0631	0.0099	0.0181	-0.0795	0.0534	-0.1098	33.9561	22.699	-10.8783
2	1.602	1.5703	2.9916	2.3063	4.4856	8.8387	-0.1107	0.0667	0.1075	-0.0208	-0.0158	0.0314	0.0058	0.2647	0.1264	0.0338	-0.0175	-0.0226	-0.0629	0.043	-0.0808	28.6631	24.2075	14.3254
3	1.3025	-0.4962	0.1893	0.912	-0.1173	1.4244	-0.0862	0.0704	0.1771	0.0128	-0.0554	-0.0853	-0.1398	0.1147	0.1416	0.0096	-0.0689	-0.002	-0.0986	0.0539	-0.0624	31.9276	29.9776	16.0083
4	1.0379	-0.7384	0.1316	1.9284	0.4552	2.3699	-0.0781	-0.1231	-0.0433	0.0109	0.0623	-0.0165	0.1254	0.1708	0.0158	-0.0529	0.0195	-0.0386	-0.0529	0.0395	-0.0882	37.0523	11.9579	48.5759
5	3.2054	1.4687	3.2528	1.0538	1.2412	3.464	-0.0844	0.1203	-0.0075	0.0109	0.0958	-0.0383	0.1805	0.1688	-0.0114	0.0028	-0.0005	-0.0407	-0.0443	0.0206	-0.0572	28.054	20.2874	25.9682
6	1.1638	0.0035	-0.3481	1.3169	0.0418	1.3817	-0.049	-0.0058	-0.0474	0.035	-0.0917	0.0964	0.1685	-0.0663	0.1407	-0.0191	-0.0295	-0.0267	-0.1013	0.0568	-0.0938	23.4771	15.3374	24.5567
7	2.6346	0.0825	0.339	0.7129	-0.3738	2.6175	0.1104	0.1158	0.0406	-0.0892	-0.0656	0.0199	-0.098	-0.0942	-0.0448	-0.0622	0.0107	-0.0506	-0.0976	0.0237	-0.0936	-7.8273	41.0259	-3.9204
8	0.7548	-0.0335	0.1605	3.8576	-5.1788	6.9702	-0.1402	0.0648	0.0466	-0.0998	0.0574	-0.0939	0.085	-0.3782	0.0828	-0.0073	-0.0371	-0.0356	-0.0366	0.0224	-0.0563	3.7634	36.6212	18.6183
9	1.0725	0.1111	0.2992	1.3147	-0.2378	2.1068	0.0068	-0.0268	-0.0991	-0.0802	-0.0318	-0.0017	0.2865	-0.1284	0.025	-0.0466	-0.0653	-0.0818	-0.1215	0.005	-0.0763	0.8982	30.6045	20.3101
10	1.0894	0.1734	0.3995	1.2699	0.1584	2.3169	-0.0509	-0.187	0.0967	0.0875	-0.0035	0.052	-0.0322	-0.1879	0.0545	-0.0744	-0.0301	-0.0253	0.0393	-0.0463	-0.0991	4.7797	43.8813	55.1746
11	0.5246	0.0573	-0.2165	0.9908	-0.9	1.0814	-0.1511	0.0182	0.1822	0.0241	0.02	-0.0592	-0.0725	-0.2112	0.1311	0.0069	-0.0116	-0.0347	-0.0234	-0.0175	-0.0841	7.4558	39.002	30.1169
12	1.1724	-0.2105	0.1077	1.1965	-0.6051	1.5361	0.0226	-0.0329	0.1075	-0.0135	-0.1249	-0.1738	-0.105	0.0671	0.1023	-0.0319	-0.049	-0.0465	-0.0797	-0.0149	-0.0796	11.5606	44.1294	28.1805

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	262 - 429
2	X-RAY DIFFRACTION	2	A	430 - 460
3	X-RAY DIFFRACTION	3	A	461 - 553
4	X-RAY DIFFRACTION	4	B	262 - 429
5	X-RAY DIFFRACTION	5	B	430 - 460
6	X-RAY DIFFRACTION	6	B	461 - 553
7	X-RAY DIFFRACTION	7	C	262 - 429
8	X-RAY DIFFRACTION	8	C	430 - 460
9	X-RAY DIFFRACTION	9	C	461 - 553
10	X-RAY DIFFRACTION	10	D	262 - 429
11	X-RAY DIFFRACTION	11	D	430 - 460
12	X-RAY DIFFRACTION	12	D	461 - 553

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