PDB-4qns: Crystal structure of bromodomain from Plasmodium faciparum GCN5, ...

ID or keywords:

Entry

Database: PDB / ID: 4qns

Title

Crystal structure of bromodomain from Plasmodium faciparum GCN5, PF3D7_0823300

Components

Histone acetyltransferase GCN5, putative

Keywords

TRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / bromodomain / histone / malaria

Function / homology

Function and homology information

: / histone H3 acetyltransferase activity / histone acetyltransferase complex / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.497 Å

Authors

Fonseca, M. / Tallant, C. / Knapp, S. / Loppnau, P. / von Delft, F. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Structural Genomics Consortium (SGC)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of bromodomain from Plasmodium faciparum GCN5, PF3D7_0823300
Authors: Fonseca, M. / Tallant, C. / Knapp, S. / Loppnau, P. / Hui, R. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C.

History

Deposition	Jun 18, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4qns.cif.gz	200.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4qns.ent.gz	163.6 KB	Display	PDB format
PDBx/mmJSON format	4qns.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4qns_validation.pdf.gz	478.7 KB	Display	wwPDB validaton report
Full document	4qns_full_validation.pdf.gz	480.7 KB	Display
Data in XML	4qns_validation.xml.gz	22.3 KB	Display
Data in CIF	4qns_validation.cif.gz	33 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/4qns ftp://data.pdbj.org/pub/pdb/validation_reports/qn/4qns	HTTPS FTP

-
Related structure data

Similar structure data	3o6u-5 4j7z-1 3qzn-3 4j7z-5 3clx-3 6i2v-d 5o39-d 5ibn-d 1b9o-d 5oho-2 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4)

Deposited unit

A: Histone acetyltransferase GCN5, putative

B: Histone acetyltransferase GCN5, putative

C: Histone acetyltransferase GCN5, putative

D: Histone acetyltransferase GCN5, putative

hetero molecules

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

1

A: Histone acetyltransferase GCN5, putative

hetero molecules

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

2

B: Histone acetyltransferase GCN5, putative

hetero molecules

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

3

C: Histone acetyltransferase GCN5, putative

hetero molecules

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

4

D: Histone acetyltransferase GCN5, putative

hetero molecules

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

5

B: Histone acetyltransferase GCN5, putative

hetero molecules

C: Histone acetyltransferase GCN5, putative

hetero molecules

A: Histone acetyltransferase GCN5, putative

D: Histone acetyltransferase GCN5, putative

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.217, 98.871, 50.439
Angle α, β, γ (deg.)	90.000, 109.630, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

AUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

#1: Protein	Histone acetyltransferase GCN5, putative Mass: 12622.471 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: gcn5, PF08_0034, PFNF54_02299 / Plasmid: pet15mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IB67
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.34 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 2.0 M Ammonium sulfate 0.1 M sodium acetate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97623 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.97623 Å / Relative weight: 1

Reflection

Resolution: 1.5→29 Å / Num. all: 74520 / Num. obs: 74224 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / B_iso Wilson estimate: 11.74 Å² / R_merge(I) obs: 0.089 / Net I/σ(I): 13.9 / Scaling rejects: 42

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	% possible all
1.5-1.52	6.1	0.487	3.9	21749	3567	95.8
8.2-29	6.3	0.062	32.5	2966	468	97.5

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
Aimless	0.3.5	data scaling
PHASER		phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.14	data extraction
ADSC	Quantum	data collection
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.497→28.999 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 17.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1868	3595	4.85 %	random
R_work	0.1563	-	-	-
obs	0.1578	74191	99.59 %	-
all	-	74496	-	-

Solvent computation

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

Displacement parameters

B_iso max: 85.09 Å² / B_iso mean: 16.5608 Å² / B_iso min: 5.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.497→28.999 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3493	0	80	454	4027

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3856
X-RAY DIFFRACTION	f_angle_d	1.05	5233
X-RAY DIFFRACTION	f_chiral_restr	0.044	538
X-RAY DIFFRACTION	f_plane_restr	0.006	673
X-RAY DIFFRACTION	f_dihedral_angle_d	12.622	1489

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4968-1.5165	0.2366	124	0.2217	2606	2730	95
1.5165-1.5373	0.1803	121	0.1791	2694	2815	100
1.5373-1.5592	0.2235	107	0.1746	2735	2842	100
1.5592-1.5825	0.2049	145	0.165	2733	2878	100
1.5825-1.6072	0.203	152	0.1712	2725	2877	100
1.6072-1.6336	0.2261	136	0.1702	2661	2797	100
1.6336-1.6617	0.205	137	0.1698	2717	2854	100
1.6617-1.6919	0.2012	132	0.1626	2706	2838	99
1.6919-1.7245	0.1749	163	0.1633	2677	2840	100
1.7245-1.7597	0.2167	142	0.1523	2727	2869	100
1.7597-1.7979	0.1702	113	0.1439	2752	2865	100
1.7979-1.8398	0.1716	142	0.1465	2704	2846	100
1.8398-1.8858	0.1999	132	0.1475	2718	2850	100
1.8858-1.9367	0.1939	158	0.1565	2736	2894	100
1.9367-1.9937	0.2023	125	0.1564	2685	2810	100
1.9937-2.058	0.1852	139	0.1555	2755	2894	100
2.058-2.1316	0.177	130	0.1516	2714	2844	100
2.1316-2.2169	0.1655	165	0.1432	2714	2879	100
2.2169-2.3177	0.1811	136	0.1502	2710	2846	100
2.3177-2.4399	0.1659	141	0.1539	2730	2871	100
2.4399-2.5927	0.231	157	0.1638	2708	2865	100
2.5927-2.7927	0.2037	128	0.1699	2751	2879	100
2.7927-3.0734	0.1751	142	0.1688	2723	2865	100
3.0734-3.5175	0.2012	155	0.1571	2699	2854	99
3.5175-4.4292	0.1586	125	0.1343	2751	2876	99
4.4292-29.0041	0.1705	148	0.1543	2765	2913	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	4.4353	-1.7386	-2.7333	3.0871	1.4679	3.7039	-0.1019	0.0809	-0.0642	0.0152	-0.0134	0.1073	-0.0162	-0.1045	0.0079	0.0754	0.0074	-0.0199	0.091	0.0223	0.1181	-44.8151	37.4287	51.9799
2	1.1623	-0.1748	0.0751	1.9493	-0.5273	1.3395	-0.0143	-0.0289	-0.0966	-0.0096	-0.0816	-0.0994	0.149	0.1068	0.0275	0.1093	0.0086	0.0006	0.1138	0.0126	0.1132	-30.1026	21.2144	52.1418
3	1.6282	-0.759	-2.2235	2.8649	0.2299	3.3215	0.007	0.1938	-0.0252	-0.0775	0.0295	0.1529	0.0837	-0.211	-0.027	0.1104	-0.0111	-0.0123	0.0954	0.0299	0.1269	-42.4996	27.4714	54.1908
4	1.1787	-0.1029	-0.0399	1.3867	-0.0352	0.6907	-0.0928	-0.2024	-0.0143	0.1531	0.0662	-0.0994	0.0532	0.0263	-0.0119	0.0939	-0.0038	-0.0023	0.0814	0.0104	0.1103	-31.0505	31.508	56.1559
5	1.3507	-0.8046	-0.2463	2.6609	0.1395	1.0043	0.0342	0.0827	0.1058	-0.2079	-0.0082	-0.112	0.0249	-0.0849	-0.0076	0.0865	-0.0046	0.0122	0.0597	0.0004	0.0966	-28.8648	35.6852	46.5863
6	3.0883	-1.4862	-1.6255	1.2389	1.0755	1.7966	-0.0388	0.0592	0.1798	-0.0159	0.0656	-0.112	-0.0882	0.0904	-0.0223	0.0786	0.0074	-0.0122	0.1156	0.0105	0.0742	-26.2361	63.0371	24.6597
7	2.4848	0.0343	-1.1987	0.2802	0.2397	2.6376	0.004	-0.2912	0.0063	0.1634	-0.0405	0.0849	0.2123	0.1323	0.0718	0.1628	0.0012	-0.001	0.1518	0.0161	0.1573	-38.7817	60.3152	41.615
8	0.9586	-0.3629	-0.1314	0.4554	0.299	1.0503	-0.0355	0.0496	0.0173	0.0488	-0.0334	-0.0155	0.0058	0.0211	0.0642	0.0877	0.0121	-0.0095	0.0868	-0.0083	0.0689	-34.9556	60.3742	27.4403
9	3.8632	-0.8147	1.9385	2.8328	-1.1185	3.0858	-0.0706	-0.366	0.3139	0.1118	0.0509	0.0849	-0.4038	-0.259	0.0747	0.1243	0.0353	0.0019	0.1592	-0.0315	0.1274	-28.5099	68.3495	66.3287
10	0.9304	0.4276	-0.2673	0.7589	-0.3432	1.8073	-0.0014	-0.0365	0.0635	0.0112	-0.0503	-0.0632	-0.1566	0.1147	0.0439	0.0986	0.0021	-0.0092	0.0826	0.0004	0.0809	-10.4827	65.8917	59.2222
11	4.3279	-2.0421	0.6963	2.3818	-0.8839	1.702	-0.134	-0.1943	0.4467	0.0381	-0.0315	0.135	-0.28	-0.0774	0.0508	0.1452	0.0185	-0.0375	0.0999	-0.0377	0.1804	-22.8635	74.3554	62.1263
12	1.4449	2.2858	0.6471	5.2938	2.2152	1.3739	-0.2536	0.2209	0.5016	-0.2768	-0.0197	0.2987	-0.3406	-0.0905	0.1389	0.2019	0.0577	-0.0775	0.1749	0.0151	0.2465	-29.5638	75.761	56.1614
13	1.1718	0.3293	-0.1109	0.7195	-0.0879	0.8936	-0.0173	-0.0095	0.0481	0.0445	-0.0005	0.0126	-0.0304	-0.0645	0.0203	0.0682	0.0057	-0.0072	0.0688	-0.0109	0.0597	-20.1424	58.8395	59.1932
14	3.931	1.7661	-1.1122	2.5198	-0.9985	2.6615	-0.0365	0.1797	-0.5742	-0.3022	0.0561	-0.2471	0.2058	0.1376	0.041	0.1256	0.0133	0.0223	0.1114	-0.0413	0.2344	-5.5263	38.4483	42.734
15	4.2219	-0.2777	0.019	1.4748	1.3208	1.2244	0.0009	-0.231	-0.3352	0.2521	0.0419	-0.1414	0.1511	-0.063	-0.0242	0.1126	-0.0018	-0.005	0.0737	0.0079	0.1171	-19.5724	38.7469	49.9147
16	2.2244	-0.9323	0.3553	2.729	0.2144	1.3839	-0.0168	0.0259	-0.0484	-0.2254	0.0414	0.2982	-0.0616	-0.2564	0.0379	0.11	0.0281	-0.0234	0.1319	0.0227	0.0916	-25.4956	51.1715	40.6357
17	5.5187	0.579	-2.847	2.1461	-1.275	3.3343	-0.0678	0.4943	-0.4123	-0.4346	0.1881	-0.1688	0.1344	0.0586	-0.0129	0.1805	-0.0068	0.0042	0.1526	-0.061	0.1406	-11.8986	42.5053	36.2689
18	1.2065	0.1279	-0.0265	1.0045	0.2581	0.7567	-0.0251	0.0919	-0.0629	-0.0658	0.0175	-0.1046	0.0707	0.0271	-0.0283	0.0711	0.0043	0.0069	0.0615	-0.0049	0.0766	-12.7117	48.0771	48.3094

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1355 through 1374 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1375 through 1402 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1403 through 1411 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1412 through 1440 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1441 through 1460 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1355 through 1381 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1382 through 1402 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1403 through 1460 )	B
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1360 through 1373 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1374 through 1402 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1403 through 1411 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1412 through 1417 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1418 through 1460 )	C
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1359 through 1374 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1375 through 1381 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1382 through 1402 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1403 through 1411 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1412 through 1460 )	D

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
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