PDB-4ux5: Structure of DNA complex of PCG2

ID or keywords:

Entry

Database: PDB / ID: 4ux5

Title

Structure of DNA complex of PCG2

Components

5'-D(*CP*AP*AP*TP*GP*AP*CP*GP*CP*GP*TP*AP*AP*GP)-3'
5'-D(*CP*TP*TP*AP*CP*GP*CP*GP*TP*CP*AP*TP*TP*GP)-3'
TRANSCRIPTION FACTOR MBP1

Keywords

TRANSCRIPTION / VIRULENCE GENE / TRANSCRIPTION FACTOR

Function / homology

Function and homology information

conidium formation / : / MBF transcription complex / sporulation resulting in formation of a cellular spore / DNA binding / nucleus
Similarity search - Function

Biological species

MAGNAPORTHE ORYZAE (rice blast fungus)

CANDIDA ALBICANS (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.4 Å

Authors

Liu, J. / Huang, J. / Zhao, Y. / Liu, H. / Wang, D. / Yang, J. / Zhao, W. / Taylor, I.A. / Peng, Y.

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: Structural Basis of DNA Recognition by Pcg2 Reveals a Novel DNA Binding Mode for Winged Helix-Turn-Helix Domains.
Authors: Liu, J. / Huang, J. / Zhao, Y. / Liu, H. / Wang, D. / Yang, J. / Zhao, W. / Taylor, I.A. / Peng, Y.

History

Deposition	Aug 19, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 4, 2015	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ux5.cif.gz	138.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ux5.ent.gz	109 KB	Display	PDB format
PDBx/mmJSON format	4ux5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ux5_validation.pdf.gz	443.4 KB	Display	wwPDB validaton report
Full document	4ux5_full_validation.pdf.gz	444.9 KB	Display
Data in XML	4ux5_validation.xml.gz	11.6 KB	Display
Data in CIF	4ux5_validation.cif.gz	15.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ux/4ux5 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/4ux5	HTTPS FTP

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Related structure data

Similar structure data	3gc9-1 6q8z-4 4xrj-d 5o8x-1 3zdt-1 6q3w-4 4geh-1 3mvc-d 4ifc-1 6zgz-4 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
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PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

A: TRANSCRIPTION FACTOR MBP1

B: TRANSCRIPTION FACTOR MBP1

C: 5'-D(*CP*AP*AP*TP*GP*AP*CP*GP*CP*GP*TP*AP*AP*GP)-3'

D: 5'-D(*CP*TP*TP*AP*CP*GP*CP*GP*TP*CP*AP*TP*TP*GP)-3'

38.9 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)	117.360, 117.360, 65.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P42₁2

#1: Protein	TRANSCRIPTION FACTOR MBP1 / PCG2 Mass: 15189.235 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN, RESIDUES 1-138 / Source method: isolated from a natural source / Source: (natural) MAGNAPORTHE ORYZAE (rice blast fungus) / References: UniProt: G4NA99, UniProt: L7I1M8*PLUS
#2: DNA chain	5'-D(CPAPAPTPGPAPCPGPCPGPTPAPAPGP)-3' / MCB BOX DNA Mass: 4313.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) CANDIDA ALBICANS (yeast)
#3: DNA chain	5'-D(CPTPTPAPCPGPCPGPTPCPAPTPTPGP)-3' / MCB BOX DNA Mass: 4246.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) CANDIDA ALBICANS (yeast)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.31 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.4→51.6 Å / Num. obs: 21699 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 41.5 % / B_iso Wilson estimate: 42.41 Å² / R_merge(I) obs: 0.01

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Processing

Software

Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.4→51.602 Å / SU ML: 0.29 / σ(F): 0.17 / Phase error: 26.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2576	3168	9.2 %
R_work	0.2283	-	-
obs	0.231	18523	99.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.4→51.602 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1818	567	0	56	2441

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2510
X-RAY DIFFRACTION	f_angle_d	0.848	3515
X-RAY DIFFRACTION	f_dihedral_angle_d	21.319	981
X-RAY DIFFRACTION	f_chiral_restr	0.032	362
X-RAY DIFFRACTION	f_plane_restr	0.005	369

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 (%)
2.4002-2.436	0.3258	145	0.3126	1368	X-RAY DIFFRACTION	100
2.436-2.4741	0.3373	138	0.3118	1340	X-RAY DIFFRACTION	100
2.4741-2.5147	0.3124	139	0.2984	1351	X-RAY DIFFRACTION	100
2.5147-2.558	0.3802	132	0.2826	1375	X-RAY DIFFRACTION	100
2.558-2.6045	0.3433	138	0.2907	1338	X-RAY DIFFRACTION	100
2.6045-2.6546	0.2754	143	0.2715	1353	X-RAY DIFFRACTION	100
2.6546-2.7088	0.3134	137	0.2756	1378	X-RAY DIFFRACTION	100
2.7088-2.7677	0.2847	136	0.2788	1339	X-RAY DIFFRACTION	100
2.7677-2.8321	0.3314	133	0.27	1352	X-RAY DIFFRACTION	100
2.8321-2.9029	0.2516	143	0.2636	1366	X-RAY DIFFRACTION	100
2.9029-2.9814	0.3214	144	0.2619	1355	X-RAY DIFFRACTION	100
2.9814-3.0691	0.3375	138	0.2656	1355	X-RAY DIFFRACTION	100
3.0691-3.1681	0.306	141	0.252	1355	X-RAY DIFFRACTION	100
3.1681-3.2814	0.2408	134	0.2315	1367	X-RAY DIFFRACTION	100
3.2814-3.4127	0.2535	131	0.2136	1343	X-RAY DIFFRACTION	100
3.4127-3.568	0.2274	138	0.1973	1359	X-RAY DIFFRACTION	100
3.568-3.7561	0.235	141	0.2171	1376	X-RAY DIFFRACTION	100
3.7561-3.9913	0.2278	133	0.1936	1345	X-RAY DIFFRACTION	100
3.9913-4.2993	0.1483	143	0.1983	1355	X-RAY DIFFRACTION	100
4.2993-4.7317	0.2464	135	0.1767	1365	X-RAY DIFFRACTION	100
4.7317-5.4158	0.2696	137	0.2111	1360	X-RAY DIFFRACTION	100
5.4158-6.8208	0.2444	137	0.2245	1358	X-RAY DIFFRACTION	100
6.8208-51.6143	0.2621	132	0.2333	1334	X-RAY DIFFRACTION	97

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	7.9768	0.6535	3.7654	8.4373	0.3721	5.4	0.3056	0.2037	0.0206	-0.5383	0.4947	1.8473	-0.1033	-1.0973	0.8441	0.3679	-0.0676	-0.0564	0.3452	0.1411	0.5241	-3.5643	-41.7431	44.3423
2	8.2407	-0.2014	0.8539	8.0292	-0.166	0.0947	0.4575	0.2046	0.4004	-0.4272	0.0113	0.7186	0.4893	-0.7309	0.3659	0.5305	-0.0477	-0.005	0.3051	0.0963	0.3207	0.2172	-40.8446	42.4903
3	5.5416	0.865	0.2067	7.3669	0.2869	6.3385	0.1591	-0.408	0.385	0.4937	-0.0622	0.4129	-0.5453	-1.1531	0.3111	0.3592	0.0438	0.0199	0.5048	-0.0423	0.2541	0.4709	-35.6467	43.943
4	5.6131	-2.6296	-0.1165	7.2686	1.2557	3.4016	-0.2115	-0.1125	0.5535	0.5648	0.2587	-0.779	-0.6714	0.9408	0.1275	0.5852	-0.1089	-0.0416	0.5172	0.0051	0.238	10.0811	-29.9565	40.7573
5	7.8527	-4.3971	2.6967	7.1997	-0.4009	2.5565	-0.4022	-1.2799	0.3513	0.1577	-0.2334	-0.8576	0.226	1.4106	0.0215	0.573	-0.0706	0.045	0.8942	0.1883	0.3898	17.2885	-33.481	36.014
6	1.8843	-0.5541	0.345	5.4004	-2.1631	4.9979	0.1243	-0.2129	0.1637	-0.6165	-0.2966	0.1156	-0.2568	-0.1955	-0.1979	0.4217	-0.0521	-0.0036	0.3035	-0.004	0.2594	5.3769	-35.5482	34.6665
7	8.7196	0.692	0.5708	3.7898	3.5645	3.3886	-0.4432	-0.698	-0.5737	0.2573	0.1366	-0.6524	-0.8953	1.7238	0.4795	0.5641	-0.1068	-0.0876	0.677	0.0629	0.3324	15.3786	-34.8011	48.8578
8	7.6333	3.3204	-1.785	3.1232	1.4266	4.0945	0.1456	-0.671	0.5153	2.4431	-0.5239	0.1274	-0.8558	0.0212	1.0399	0.7193	-0.0853	-0.1177	0.362	0.0064	0.3421	7.6358	-34.3747	53.2635
9	8.6911	-5.0463	-2.0371	5.8679	2.4866	1.4068	-0.2129	1.0536	-1.0465	-1.9001	0.2292	-0.2979	-0.4025	0.4402	-0.6115	0.8365	-0.0497	0.1771	0.6663	-0.1033	0.5229	11.2418	-50.6043	45.988
10	5.8701	2.9439	-3.256	5.4502	-2.6508	6.8625	0.166	-0.0283	0.5366	0.4604	0.1256	0.2361	-0.8907	-0.3442	-0.0623	0.4386	-0.0332	0.0458	0.3624	0.0156	0.3164	16.316	-18.051	11.9259
11	8.1513	0.3048	1.2533	5.57	-2.3157	2.3195	-0.5479	0.0879	0.4154	0.4151	-0.0343	-0.2585	-0.9927	0.5522	-0.0408	0.4169	0.0091	-0.0462	0.3531	-0.0325	0.3209	16.0249	-22.19	12.5231
12	2.4599	-1.3277	-0.6134	5.1807	-0.3268	3.8841	-0.0676	0.5856	0.2638	-0.1611	-0.0955	0.4821	-0.621	-0.4037	-0.4328	0.5047	-0.006	-0.1082	0.4624	0.0669	0.3696	10.8187	-22.6091	10.2433
13	2.3971	-1.4759	-0.2188	8.1167	-0.775	3.5255	-0.0286	0.7525	-0.2835	-0.0661	0.0547	0.5857	0.1737	-0.015	-0.2206	0.4077	-0.0435	-0.0447	0.3514	0.0249	0.1916	10.8807	-30.4943	9.6468
14	7.8039	-5.4532	-2.9297	6.0139	2.2806	1.1101	-0.0398	-0.5594	-0.9867	0.5907	-0.1625	3.0021	0.6975	-0.2844	0.1134	0.6066	-0.1832	0.0281	0.4494	0.0233	0.8767	-0.1454	-38.147	11.7008
15	3.3501	-1.0632	1.744	3.9597	-0.1932	1.0443	0.2732	0.3308	-0.9291	0.2773	0.3381	-0.2369	0.9423	0.187	-0.1991	0.667	-0.0193	0.0098	0.3986	0.0928	0.582	11.0038	-41.18	12.7693
16	5.3805	-1.7183	-1.8316	8.9953	4.4289	4.7882	-0.0041	-0.6659	-0.0678	0.8819	-0.2741	-0.1597	-0.2739	-0.1388	0.3532	0.4471	-0.0314	-0.0449	0.4045	0.0698	0.3148	11.4012	-30.402	17.6693
17	5.7265	-0.3209	-0.1056	2.7862	-2.1803	5.7369	0.0333	1.419	-0.4696	-1.4685	-0.1343	-0.223	0.5639	1.1177	-0.8331	0.5516	0.0001	-0.0798	0.4995	-0.193	0.3408	12.706	-34.9456	0.7286
18	7.7681	2.9791	2.6851	6.3743	2.6723	1.8547	-0.8861	0.3465	0.4827	-1.7584	0.312	0.5646	-0.9623	-0.1966	-0.938	0.6166	-0.0604	-0.1004	0.4621	0.0502	0.3503	10.3767	-26.6434	-0.6715
19	5.0067	-0.5624	-0.385	8.0262	0.8969	1.6384	0.5553	0.7297	0.2446	-0.0692	0.225	-0.5124	-0.3696	-0.3466	-0.1133	0.6869	-0.1691	-0.0162	0.3915	0.0557	0.3172	21.9964	-17.9909	8.3587
20	5.9579	2.086	0.9525	2.717	0.2991	1.9823	-0.097	-0.0053	0.1065	-0.4886	0.0403	0.5576	0.0514	-0.8306	0.0097	0.5026	-0.103	-0.1493	0.5883	-0.0017	0.466	-3.5038	-28.4064	25.5517
21	4.7802	0.3613	0.1441	5.7955	1.6564	1.6391	-0.3267	0.3953	0.0687	-1.251	0.2747	0.5247	-0.3406	-0.2941	-0.5378	0.5899	-0.0944	-0.1404	0.4693	0.0514	0.4311	-0.8065	-27.9702	24.5165

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 14 THROUGH 22 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 23 THROUGH 32 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 33 THROUGH 43 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 44 THROUGH 71 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 72 THROUGH 81 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 82 THROUGH 94 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 95 THROUGH 104 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 105 THROUGH 116 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 117 THROUGH 128 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 14 THROUGH 22 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 23 THROUGH 32 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 33 THROUGH 43 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 44 THROUGH 61 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 62 THROUGH 71 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 72 THROUGH 81 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 82 THROUGH 94 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 95 THROUGH 104 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 105 THROUGH 115 )
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 116 THROUGH 128 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 1 THROUGH 14 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 1 THROUGH 14 )

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi