PDB-4njk: Crystal Structure of QueE from Burkholderia multivorans in comple...

ID or keywords:

Entry

Database: PDB / ID: 4njk

Title

Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 7-carboxy-7-deazaguanine, and Mg2+

Components

7-carboxy-7-deazaguanine synthase

Keywords

LYASE / AdoMet radical enzyme / modified partial TIM barrel-like structure / radical SAM fold / radical AdoMet fold / synthase

Function / homology

Function and homology information

7-carboxy-7-deazaguanine synthase / carbon-nitrogen lyase activity / queuosine biosynthetic process / S-adenosyl-L-methionine binding / 4 iron, 4 sulfur cluster binding / magnesium ion binding / protein homodimerization activity / identical protein binding
Similarity search - Function

Biological species

Burkholderia multivorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.911 Å

Authors

Dowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L.

Citation

Journal: Nat.Chem.Biol. / Year: 2014
Title: Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism.
Authors: Dowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L.

History

Deposition	Nov 10, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2014	Group: Database references
Revision 1.2	Feb 5, 2014	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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	4njk.cif.gz	198.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4njk.ent.gz	157.4 KB	Display	PDB format
PDBx/mmJSON format	4njk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4njk_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4njk_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4njk_validation.xml.gz	22.8 KB	Display
Data in CIF	4njk_validation.cif.gz	34 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nj/4njk ftp://data.pdbj.org/pub/pdb/validation_reports/nj/4njk	HTTPS FTP

-
Related structure data

Related structure data	4njgSC 4njhC 4njiC 4njjC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2uvg-d 1wak-d 4nji-d 3vse-1 4jxi-2 4jf9-d 4ik1-d 2evi-d 6s68-1 3sg4-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: 7-carboxy-7-deazaguanine synthase

B: 7-carboxy-7-deazaguanine synthase

hetero molecules

52.8 kDa, 2 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)	118.790, 118.790, 102.664
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-435- HOH

-
Protein , 1 types, 2 molecules AB

#1: Protein	7-carboxy-7-deazaguanine synthase / CDG synthase / Queuosine biosynthesis protein QueE Mass: 25343.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / 249 / Gene: queE, Bmul_3115, BMULJ_00116 / Production host: Escherichia coli (E. coli) References: UniProt: A9AC61, UniProt: A0A0H3KB22*PLUS, 7-carboxy-7-deazaguanine synthase

#1: Protein

7-carboxy-7-deazaguanine synthase / CDG synthase / Queuosine biosynthesis protein QueE

Mass: 25343.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / 249 / Gene: queE, Bmul_3115, BMULJ_00116 / Production host:

Escherichia coli (E. coli)
References: UniProt: A9AC61, UniProt: A0A0H3KB22*PLUS, 7-carboxy-7-deazaguanine synthase

-
Non-polymers , 7 types, 457 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#4: Chemical	ChemComp-2KA / 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid Mass: 194.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆N₄O₃
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 446 / 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: 3.57 Å³/Da / Density % sol: 65.57 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: anaerobic, 1.8 M sodium dipotassium phosphate, pH 6.8, 0.1 M acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2013
Radiation	Monochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.91→47.2 Å / Num. obs: 55525 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / B_iso Wilson estimate: 34.8 Å² / R_sym value: 0.054 / Net I/σ(I): 29.2
Reflection shell	Resolution: 1.91→1.98 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.8 / R_sym value: 0.575 / % possible all: 94.7

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NJG

4njg

Resolution: 1.911→47.182 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 18.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1832	2745	4.95 %
R_work	0.1528	-	-
obs	0.1543	55489	96.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.911→47.182 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3240	0	111	446	3797

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3533
X-RAY DIFFRACTION	f_angle_d	1.522	4848
X-RAY DIFFRACTION	f_dihedral_angle_d	13.903	1340
X-RAY DIFFRACTION	f_chiral_restr	0.074	512
X-RAY DIFFRACTION	f_plane_restr	0.008	689

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 (%)
1.9105-1.9435	0.2642	125	0.2336	2478	X-RAY DIFFRACTION	93
1.9435-1.9788	0.2034	130	0.2143	2575	X-RAY DIFFRACTION	95
1.9788-2.0169	0.2485	146	0.194	2555	X-RAY DIFFRACTION	96
2.0169-2.058	0.2284	136	0.1917	2625	X-RAY DIFFRACTION	98
2.058-2.1028	0.2423	145	0.1872	2611	X-RAY DIFFRACTION	98
2.1028-2.1517	0.2264	124	0.1822	2646	X-RAY DIFFRACTION	97
2.1517-2.2055	0.2108	153	0.1778	2503	X-RAY DIFFRACTION	94
2.2055-2.2651	0.2146	152	0.1631	2595	X-RAY DIFFRACTION	97
2.2651-2.3318	0.1956	140	0.1607	2654	X-RAY DIFFRACTION	98
2.3318-2.407	0.2243	139	0.159	2651	X-RAY DIFFRACTION	99
2.407-2.4931	0.1897	143	0.1575	2665	X-RAY DIFFRACTION	98
2.4931-2.5929	0.1833	116	0.1665	2662	X-RAY DIFFRACTION	98
2.5929-2.7109	0.252	135	0.1722	2549	X-RAY DIFFRACTION	94
2.7109-2.8538	0.1864	116	0.166	2722	X-RAY DIFFRACTION	99
2.8538-3.0325	0.2271	134	0.1673	2685	X-RAY DIFFRACTION	99
3.0325-3.2666	0.1819	169	0.1677	2665	X-RAY DIFFRACTION	98
3.2666-3.5953	0.1679	113	0.1495	2610	X-RAY DIFFRACTION	94
3.5953-4.1152	0.155	145	0.1241	2743	X-RAY DIFFRACTION	99
4.1152-5.1837	0.1279	145	0.1142	2681	X-RAY DIFFRACTION	96
5.1837-47.1963	0.1804	139	0.1531	2869	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	5.6171	0.6732	1.6756	1.235	-0.8376	3.4588	0.1463	0.737	-0.4956	-0.2315	-0.0665	-0.3398	0.2912	0.4542	-0.0697	0.268	0.008	0.0185	0.3508	-0.1434	0.3304	16.8998	80.6339	3.2908
2	4.199	-5.4991	4.0465	7.7879	-6.8641	9.9074	0.1188	0.5409	-0.4561	-0.2651	0.0582	0.115	0.5134	0.1924	-0.3372	0.2824	-0.0496	0.0696	0.4394	-0.194	0.4527	18.5092	75.7968	2.0069
3	2.0577	0.5458	0.8296	2.2894	0.3256	2.7906	-0.1526	0.9193	0.0935	-0.5732	0.1137	-0.1084	-0.2356	0.4508	0.0288	0.3468	-0.0432	0.0178	0.505	0.0084	0.2304	13.3026	91.0498	-3.2451
4	9.9603	-7.3277	7.6992	6.943	-4.9897	3.2348	-0.006	0.3428	0.7578	-0.5882	-0.3616	-0.793	0.288	0.4142	0.4951	0.2601	0.0031	0.0077	0.3156	-0.027	0.2939	18.2992	92.1775	10.4135
5	4.8389	-1.1744	1.5999	4.6132	-2.0044	2.4335	-0.1849	-0.1546	0.0996	0.3964	-0.0108	-0.2973	-0.2791	-0.059	0.1891	0.2143	-0.0184	-0.0415	0.2538	-0.0438	0.2233	18.9514	89.382	20.4551
6	4.6343	-5.4283	0.121	9.718	-0.7963	2.7957	-0.0677	-0.2353	-0.4978	-0.4453	0.2256	0.5527	0.2508	-0.2552	-0.076	0.2044	-0.0494	-0.0859	0.3332	-0.0098	0.2915	10.5535	78.3766	20.6461
7	2.6204	-0.9903	-1.1317	3.5484	3.2927	8.1146	0.0364	-0.2551	-0.1821	0.0632	-0.0256	0.0473	-0.0082	-0.4367	-0.0434	0.154	0.0238	-0.024	0.2734	0.0146	0.2192	6.7545	81.4663	19.3791
8	2.4296	0.1264	0.9165	1.3311	0.1717	1.4394	0.0093	-0.6577	0.1937	0.2823	-0.1093	0.3	-0.0247	-0.2994	0.111	0.259	0.0303	0.0338	0.4787	-0.0748	0.2801	-11.0465	85.5867	27.6016
9	6.1745	-2.671	6.329	9.7118	-4.1404	8.4041	0.0454	-0.3637	-0.1752	0.5379	0.199	0.9908	0.2232	-0.7237	-0.3014	0.2903	0.0008	0.0755	0.4407	-0.093	0.4347	-24.6901	76.795	20.2976
10	1.2242	0.5055	1.7659	2.1844	3.7216	4.046	-0.0213	-1.4274	-0.034	0.2747	-0.342	0.8682	-0.2061	-0.3816	0.2464	0.4661	-0.0412	0.1206	0.9309	-0.1027	0.4956	-15.9523	85.119	37.6463
11	2.6331	-0.1621	0.5425	1.2965	0.5548	2.7682	-0.1109	-0.6592	0.441	0.1868	-0.0955	0.1945	-0.2938	-0.198	0.2233	0.2594	0.0197	-0.0245	0.4031	-0.1523	0.3262	-12.0427	92.8532	23.4461
12	3.7468	1.3921	-1.4299	2.347	-3.6797	4.1001	-0.2109	-0.1449	0.3146	-0.1486	0.0649	-0.2301	-0.2788	0.0065	0.1225	0.2695	0.0248	-0.1048	0.2567	-0.104	0.309	-11.7292	89.7139	8.4826
13	8.0426	7.8328	-6.9186	2.618	-7.3176	7.6013	-0.2048	0.5325	-0.3317	-0.4223	0.2642	0.1951	0.4011	-0.2085	0.0662	0.3021	0.0352	-0.0558	0.341	-0.1204	0.3399	-8.2398	78.2391	3.4772
14	2.0821	-0.1118	0.0751	2.0642	-1.7045	3.5433	0.0836	-0.1402	-0.2014	-0.0838	-0.0041	0.0454	0.1543	0.3252	-0.0671	0.214	-0.0101	-0.0303	0.301	-0.0592	0.2659	-3.8966	80.6159	15.2277

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain B and resid 2:46)
2	X-RAY DIFFRACTION	2	(chain B and resid 47:60)
3	X-RAY DIFFRACTION	3	(chain B and resid 61:123)
4	X-RAY DIFFRACTION	4	(chain B and resid 124:139)
5	X-RAY DIFFRACTION	5	(chain B and resid 140:167)
6	X-RAY DIFFRACTION	6	(chain B and resid 168:189)
7	X-RAY DIFFRACTION	7	(chain B and resid 190:210)
8	X-RAY DIFFRACTION	8	(chain A and resid 2:36)
9	X-RAY DIFFRACTION	9	(chain A and resid 37:51)
10	X-RAY DIFFRACTION	10	(chain A and resid 52:68)
11	X-RAY DIFFRACTION	11	(chain A and resid 69:158)
12	X-RAY DIFFRACTION	12	(chain A and resid 159:177)
13	X-RAY DIFFRACTION	13	(chain A and resid 178:195)
14	X-RAY DIFFRACTION	14	(chain A and resid 196:210)

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 7 types, 457 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 7 types, 457 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 7 types, 457 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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