PDB-3rj4: Crystal Structure of 7-cyano-7-deazaguanine Reductase, QueF from ...

ID or keywords:

Entry

Database: PDB / ID: 3rj4

Title

Crystal Structure of 7-cyano-7-deazaguanine Reductase, QueF from Vibrio cholerae

Components

7-cyano-7-deazaguanine Reductase QueF

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / tunnelling fold / Rossman-fold / reductase / cytosol

Function / homology

Function and homology information

preQ1 synthase / preQ1 synthase activity / queuosine biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Kim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal Structure of 7-cyano-7-deazaguanine Reductase, QueF from Vibrio cholerae
Authors: Kim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / CSGID

History

Deposition	Apr 15, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2011	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3rj4.cif.gz	227 KB	Display	PDBx/mmCIF format
PDB format	pdb3rj4.ent.gz	192.7 KB	Display	PDB format
PDBx/mmJSON format	3rj4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3rj4_validation.pdf.gz	464.3 KB	Display	wwPDB validaton report
Full document	3rj4_full_validation.pdf.gz	473.7 KB	Display
Data in XML	3rj4_validation.xml.gz	26.3 KB	Display
Data in CIF	3rj4_validation.cif.gz	38 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rj/3rj4 ftp://data.pdbj.org/pub/pdb/validation_reports/rj/3rj4	HTTPS FTP

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Related structure data

Related structure data	3bp1 4iqi
Similar structure data	3rzp-d 3s19-d 3bp1-d 3m6v-d 3uxj-d 6j0v-d 6s04-d 2bra-d 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
Other databases	TargetDB: IDP01750

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (1)

Deposited unit

A: 7-cyano-7-deazaguanine Reductase QueF

B: 7-cyano-7-deazaguanine Reductase QueF

hetero molecules

66.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 7-cyano-7-deazaguanine Reductase QueF

B: 7-cyano-7-deazaguanine Reductase QueF

hetero molecules

A: 7-cyano-7-deazaguanine Reductase QueF

B: 7-cyano-7-deazaguanine Reductase QueF

hetero molecules

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

2

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	123.405, 71.841, 81.935
Angle α, β, γ (deg.)	90.00, 131.74, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-503- HOH

#1: Protein	7-cyano-7-deazaguanine Reductase QueF Mass: 33283.262 Da / Num. of mol.: 2 / Mutation: C194A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: queF / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9KTK0*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE SEQUENCE REFERENCE DOES NOT EXIST IN UNIPROT, THUS IS SELF-REFERENCED. AUTHOR INDICATED THE ...THE SEQUENCE REFERENCE DOES NOT EXIST IN UNIPROT, THUS IS SELF-REFERENCED. AUTHOR INDICATED THE GENBANK REFEREINCE OF GI 9655358 AND ACCESSION AAF94064, AND A MUTATION OF CYS-194 TO ALA-194

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.58 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Lithium sulfate, 0.1 M TRIS pH 8.5, 16 % (w/v) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2010 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97921 Å / Relative weight: 1
Reflection	Resolution: 1.715→50 Å / Num. all: 53457 / Num. obs: 53457 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / B_iso Wilson estimate: 23.62 Å² / R_sym value: 0.085 / Net I/σ(I): 18.1
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 8.2 / Num. unique all: 2675 / R_sym value: 0.303 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELXS		phasing
MLPHARE		phasing
BUCCANEER		model building
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
BUCCANEER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→35.067 Å / SU ML: 0.16 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.191	2709	5.08 %	random
R_work	0.161	-	-	-
all	0.163	53353	-	-
obs	0.163	53353	98.97 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.754 Å² / k_sol: 0.347 e/Å³

Displacement parameters

B_iso mean: 28.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.0228 Å²	-0 Å²	-1.4596 Å²
2-	-	2.5798 Å²	0 Å²
3-	-	-	0.443 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→35.067 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4129	0	13	447	4589

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4426
X-RAY DIFFRACTION	f_angle_d	1.27	6042
X-RAY DIFFRACTION	f_dihedral_angle_d	15.433	1654
X-RAY DIFFRACTION	f_chiral_restr	0.105	647
X-RAY DIFFRACTION	f_plane_restr	0.007	818

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
1.7501-1.7819	0.2489	136	0.2074	2416	2552	90
1.7819-1.8162	0.2337	147	0.2022	2632	2779	99
1.8162-1.8533	0.2289	151	0.1786	2651	2802	99
1.8533-1.8935	0.2093	146	0.175	2659	2805	99
1.8935-1.9376	0.2	146	0.1572	2696	2842	100
1.9376-1.986	0.1738	124	0.1479	2675	2799	100
1.986-2.0397	0.1855	134	0.1483	2702	2836	100
2.0397-2.0997	0.2043	146	0.1553	2679	2825	100
2.0997-2.1675	0.2009	150	0.1589	2673	2823	100
2.1675-2.245	0.2029	131	0.1595	2664	2795	100
2.245-2.3348	0.1959	166	0.1658	2655	2821	100
2.3348-2.4411	0.2237	132	0.1623	2700	2832	100
2.4411-2.5697	0.1903	131	0.176	2716	2847	100
2.5697-2.7307	0.2332	165	0.1749	2659	2824	100
2.7307-2.9414	0.2061	129	0.1766	2708	2837	100
2.9414-3.2372	0.1806	132	0.1727	2736	2868	100
3.2372-3.7052	0.1845	152	0.1486	2673	2825	100
3.7052-4.6665	0.1486	136	0.1356	2715	2851	100
4.6665-35.0741	0.1841	155	0.1658	2635	2790	95

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	0.7305	0.0277	-0.1433	0.465	-0.3226	0.7381	0.0009	0.0699	0.0717	-0.0051	0.003	0.0557	-0.0679	-0.1189	-0.0142	0.1713	0.0172	0.0062	0.1651	0.0133	0.1595	13.9595	60.2654	10.3534
2	0.6834	-0.0602	0.1724	1.0359	0.0825	0.4013	0.0458	-0.0023	-0.1161	0.0122	0.0189	0.1061	0.0412	-0.1458	-0.0335	0.1635	-0.022	-0.0063	0.2221	0.0222	0.1898	0.1172	39.5727	24.7314
3	0.5248	0.0062	0.0139	0.687	-0.1774	0.3951	0.0549	-0.0189	0.0078	-0.059	0.006	0.1072	-0.0172	-0.1256	-0.0275	0.1618	-0.003	-0.0018	0.1775	0.0095	0.1557	1.7845	47.2861	20.6683
4	0.3301	0.0484	-0.1173	0.3383	-0.0314	0.1918	-0.0377	0.1506	-0.0426	-0.0955	0.067	-0.0099	0.0269	0.0011	-0.0035	0.2194	-0.0256	0.015	0.2245	-0.0622	0.2075	31.4847	29.8158	6.6699
5	0.1653	0.2233	-0.02	0.5567	-0.0825	0.2367	-0.0879	0.1194	0.051	-0.056	0.0834	-0.0515	0.0663	0.043	-0.0184	0.1639	-0.0052	0.013	0.1833	-0.0253	0.222	33.312	35.7024	15.6052
6	0.5141	0.0078	-0.1309	0.2479	0.0308	0.4279	-0.0247	-0.0475	-0.1382	0.0173	0.0049	0.0463	0.0875	-0.0275	0.0211	0.1789	-0.0069	0.0003	0.1441	-0.0019	0.1828	22.1334	30.5137	20.4882
7	0.6466	0.016	-0.1141	0.4703	0.0398	0.4314	-0.0123	-0.0993	0.1058	-0.1065	0.0156	-0.0375	-0.0867	0.12	0.0075	0.1784	-0.0267	-0.0227	0.2027	0.0277	0.1812	39.1117	59.1368	13.1243
8	0.602	0.0445	-0.1587	0.558	-0.057	0.3667	-0.0298	0.1528	-0.0465	-0.1369	0.0347	-0.0618	-0.0331	0.1889	0.0124	0.188	-0.0475	-0.0093	0.1979	0.0191	0.1739	44.6067	54.1282	13.0479
9	0.401	0.1105	-0.106	0.8203	-0.0501	0.1375	-0.0126	0.0829	-0.0387	-0.2444	-0.0245	-0.0641	-0.0429	0.0754	0.0112	0.1916	-0.0345	-0.0207	0.1769	0.0156	0.1294	41.5671	53.0704	11.0149
10	0.2424	-0.2471	0.0961	0.3142	0.0064	0.2692	0.06	0.0772	-0.117	-0.0737	0.0129	0.0596	0.041	0.0654	0.079	0.179	-0.0089	-0.0006	0.1632	-0.0278	0.1848	45.5413	44.5313	9.5912
11	0.5987	0.2809	-0.1949	0.3506	-0.1582	0.3748	-0.0807	-0.118	-0.084	0.0284	0.0657	-0.0523	-0.0046	0.1152	0.0158	0.1568	-0.0013	-0.0094	0.1769	-0.0002	0.186	36.3787	44.1677	19.4413

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 29:147)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 148:215)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 216:287)
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 29:47)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 48:70)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 71:147)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 148:167)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 168:200)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 201:232)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 233:248)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 249:287)

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