PDB-4ghm: Crystal Structure of the H233A mutant of 7-cyano-7-deazaguanine r...

ID or keywords:

Entry

Database: PDB / ID: 4ghm

Title

Crystal Structure of the H233A mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ0

Components

NADPH-dependent 7-cyano-7-deazaguanine reductase

Keywords

OXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / tunneling fold

Function / homology

Function and homology information

preQ1 synthase / preQ1 synthase activity / tRNA modification / tRNA queuosine(34) biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.618 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 the H233A mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ0
Authors: Kim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Aug 8, 2012	Deposition site: RCSB / Processing site: RCSB
Supersession	Sep 5, 2012	ID: 3RZQ
Revision 1.0	Sep 5, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ghm.cif.gz	238.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4ghm.ent.gz	192.8 KB	Display	PDB format
PDBx/mmJSON format	4ghm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ghm_validation.pdf.gz	467.5 KB	Display	wwPDB validaton report
Full document	4ghm_full_validation.pdf.gz	474.3 KB	Display
Data in XML	4ghm_validation.xml.gz	26.8 KB	Display
Data in CIF	4ghm_validation.cif.gz	39.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gh/4ghm ftp://data.pdbj.org/pub/pdb/validation_reports/gh/4ghm	HTTPS FTP

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Related structure data

Related structure data	3bp1S 3rj4 3rzp 4iqi S: Starting model for refinement
Similar structure data	3bp1-3 3uxv-2 3uxj-2 3uxv-1 3uxj-1 5z2c-8 3s19-2 5z2c-6 6blr-d 5z2c-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
Other databases	TargetTrack: CSGID-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: NADPH-dependent 7-cyano-7-deazaguanine reductase

B: NADPH-dependent 7-cyano-7-deazaguanine reductase

hetero molecules

67.2 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)	123.114, 72.256, 81.755
Angle α, β, γ (deg.)	90.00, 131.26, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-596- HOH

#1: Protein	NADPH-dependent 7-cyano-7-deazaguanine reductase / QueF / 7-cyano-7-carbaguanine reductase / NADPH-dependent nitrile oxidoreductase / PreQ(0) reductase Mass: 33248.258 Da / Num. of mol.: 2 / Mutation: H233A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: queF, VC_0902 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9KTK0, preQ1 synthase
#2: Chemical	ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE Mass: 179.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₉N₅O
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.16 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350, 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: 0.97929 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2010 / Details: mirrors
Radiation	Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 1.618→50 Å / Num. all: 68104 / Num. obs: 68104 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / B_iso Wilson estimate: 14.2 Å² / R_sym value: 0.073 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.618→1.65 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3023 / R_sym value: 0.403 / % possible all: 89.2

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
HKL-3000		phasing
MOLREP		phasing
PHENIX	(phenix.refine: 1.8_1055)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BP1

3bp1

Resolution: 1.618→40.877 Å / SU ML: 0.14 / Isotropic thermal model: MIXED / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18	3439	5.06 %	RANDOM
R_work	0.15	-	-	-
obs	0.152	67986	98.85 %	-
all	-	67986	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.618→40.877 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4150	0	45	478	4673

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4570
X-RAY DIFFRACTION	f_angle_d	1.15	6252
X-RAY DIFFRACTION	f_dihedral_angle_d	15.796	1701
X-RAY DIFFRACTION	f_chiral_restr	0.08	672
X-RAY DIFFRACTION	f_plane_restr	0.006	844

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 (%)
1.618-1.6397	0.2834	129	0.2304	2157	2286	84
1.6397-1.6631	0.2542	136	0.2119	2419	2555	93
1.6631-1.6879	0.2306	129	0.1958	2537	2666	98
1.6879-1.7143	0.2196	146	0.1864	2588	2734	99
1.7143-1.7424	0.1976	138	0.1754	2591	2729	100
1.7424-1.7725	0.207	141	0.1672	2579	2720	100
1.7725-1.8047	0.1883	143	0.1607	2588	2731	100
1.8047-1.8394	0.2262	125	0.1625	2619	2744	100
1.8394-1.877	0.213	157	0.1608	2552	2709	100
1.877-1.9178	0.2044	140	0.1479	2601	2741	100
1.9178-1.9624	0.1683	148	0.141	2595	2743	100
1.9624-2.0114	0.1616	132	0.1385	2609	2741	100
2.0114-2.0658	0.1811	142	0.1407	2603	2745	100
2.0658-2.1266	0.199	127	0.1468	2619	2746	100
2.1266-2.1953	0.1778	147	0.1466	2590	2837	100
2.1953-2.2737	0.1741	122	0.1449	2614	2736	100
2.2737-2.3647	0.1932	148	0.148	2610	2758	100
2.3647-2.4723	0.1903	128	0.1478	2643	2771	100
2.4723-2.6027	0.1932	127	0.1562	2598	2725	100
2.6027-2.7657	0.1841	144	0.1526	2638	2782	100
2.7657-2.9792	0.1733	136	0.1548	2630	2766	100
2.9792-3.2789	0.1671	139	0.1515	2617	2756	100
3.2789-3.7531	0.1501	150	0.1348	2611	2761	100
3.7531-4.7273	0.1362	141	0.1242	2642	2783	100
4.7273-40.8898	0.1886	124	0.1562	2697	2821	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	4.6054	4.1172	-2.0757	3.9015	-1.2183	2.6575	-0.1715	0.3434	-0.1624	-0.1573	0.1724	-0.015	0.2281	-0.1004	0.0362	0.1565	0.0087	-0.0117	0.1063	-0.0367	0.1261	29.6371	-12.1982	7.3855
2	3.8254	1.6977	-0.4435	1.5453	-0.4053	0.6874	-0.0554	0.0336	-0.1159	-0.0974	0.0512	-0.0327	0.1101	0.0063	0.0366	0.1413	0.003	-0.0129	0.082	-0.018	0.0971	29.3874	-7.5482	17.509
3	1.077	-0.2099	-0.3326	0.4771	0.1962	0.7286	-0.0462	0.0006	-0.1431	-0.0042	0.0362	0.0328	0.1265	-0.0364	0.0115	0.1256	-0.0159	-0.005	0.083	0.0064	0.1142	23.71	-10.3033	19.977
4	2.0219	0.9082	-0.6142	2.5481	-1.5982	4.2525	0.0141	-0.0107	0.1777	0.0796	-0.0523	-0.0039	-0.4466	0.245	0.0361	0.1137	-0.0043	-0.02	0.0995	0.0098	0.1468	38.9681	19.6624	12.5776
5	2.5462	-0.2134	0.2156	0.7064	-0.4613	2.2581	0.0154	0.1636	-0.1276	-0.1099	-0.0033	-0.0295	-0.008	0.0816	-0.0058	0.117	-0.0168	-0.0015	0.065	0.0003	0.0972	41.4284	10.9516	12.2513
6	1.9555	0.2273	-0.0912	0.725	-0.2576	0.68	-0.0437	0.0715	-0.0351	-0.0262	0.0249	-0.0379	-0.0144	0.0673	0.0162	0.1084	-0.0077	-0.0078	0.0967	-0.0085	0.0843	40.4655	6.2162	14.2299
7	2.6451	2.2505	-1.7134	2.2507	-0.7809	2.4489	-0.1963	0.6672	-0.0698	-0.1785	0.2303	0.0433	0.1827	-0.5673	0.0357	0.1412	-0.0077	-0.039	0.2507	0.0328	0.1296	5.4949	14.694	2.8473
8	2.7587	0.7782	-0.7744	1.3922	-0.6646	1.3379	-0.1282	-0.0299	-0.0305	-0.0711	0.0652	0.1565	0.0117	-0.178	0.1027	0.1221	0.0157	-0.0216	0.1102	-0.0066	0.1068	12.0334	18.0704	12.56
9	3.4242	0.5166	-0.3796	0.4487	-0.205	0.997	0.0286	0.0834	0.1589	-0.0021	0.0156	0.0431	-0.1024	-0.116	-0.0445	0.1204	0.0164	-0.0003	0.097	0.0296	0.0956	16.6566	20.9286	8.1332
10	1.3207	-1.4655	2.1541	1.8755	-2.221	3.6224	-0.0533	-0.1023	-0.0374	0.147	0.0615	0.0954	-0.1775	-0.1651	0.0006	0.1845	0.0113	-0.0008	0.1426	-0.0159	0.1498	18.2747	21.0153	19.8732
11	2.402	2.9216	0.6949	5.8916	1.2671	2.5209	0.1626	-0.1819	-0.1311	0.3852	-0.0887	0.1337	0.2039	-0.2458	-0.0342	0.0904	0.0035	-0.0062	0.2039	0.0566	0.1812	3.6734	-5.3918	27.3388
12	1.9768	0.1894	0.4257	2.7099	0.4684	1.0093	-0.0418	0.1476	-0.0229	-0.1284	0.0862	0.2249	0.0574	-0.2858	-0.037	0.1279	-0.0324	-0.0199	0.2172	0.0577	0.139	-0.491	-0.2028	20.5124
13	6.9031	-2.9116	-4.5529	3.1973	2.5763	4.5684	0.0888	-0.1421	0.217	0.0126	0.1052	0.0537	-0.0555	-0.1897	-0.1178	0.1094	0.0048	-0.0007	0.1573	0.0357	0.0907	2.4651	4.0385	24.724
14	2.948	0.2972	-0.8829	3.4034	-1.1845	1.0436	-0.0272	0.1025	-0.1221	-0.1099	0.0605	0.2686	0.0427	-0.1828	-0.0392	0.122	-0.0449	-0.0346	0.2247	0.0211	0.144	-3.0395	0.7474	19.5911
15	7.2681	-0.7278	-2.8522	1.6128	0.2285	2.3675	0.0294	-0.0139	0.1783	0.037	0.0194	0.07	-0.0342	-0.2051	0.0096	0.0779	-0.0049	-0.009	0.1195	0.013	0.0655	4.8069	9.3243	20.4106
16	7.4177	-1.4479	0.7051	1.4549	-0.3481	0.1529	-0.1318	-0.5187	0.6694	0.2104	0.1426	-0.0883	-0.1267	-0.1864	-0.0196	0.1777	0.0146	0.0289	0.1931	-0.0198	0.1527	8.0912	13.3444	26.0321

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 29 through 47 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 48 through 75 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 147 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 148 through 167 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 168 through 212 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 213 through 287 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 29 through 48 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 49 through 75 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 76 through 128 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 129 through 147 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 148 through 167 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 168 through 199 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 200 through 212 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 213 through 248 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 249 through 272 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 273 through 287 )

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