PDB-4xcw: Crystal structure of molybdenum cofactor biosynthesis protein Mog...

ID or keywords:

Entry

Database: PDB / ID: 4xcw

Title

Crystal structure of molybdenum cofactor biosynthesis protein MogA from Helicobacter pylori str. J99

Components

Molybdopterin adenylyltransferase

Keywords

TRANSFERASE / molybdenum cofactor / molybdopterin / MPT / probable molybdopterin binding domain / alpha and beta protein / Molybdenum cofactor biosynthesis protein fold / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / Mo-molybdopterin cofactor biosynthetic process / ATP binding
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Stogios, P.J. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: To be published
Authors: Stogios, P.J. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 18, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xcw.cif.gz	444.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4xcw.ent.gz	370.6 KB	Display	PDB format
PDBx/mmJSON format	4xcw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4xcw_validation.pdf.gz	462.9 KB	Display	wwPDB validaton report
Full document	4xcw_full_validation.pdf.gz	471.1 KB	Display
Data in XML	4xcw_validation.xml.gz	50.9 KB	Display
Data in CIF	4xcw_validation.cif.gz	74.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xc/4xcw ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xcw	HTTPS FTP

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Related structure data

Related structure data	2qq1S S: Starting model for refinement
Similar structure data	1sxg-2 3mcj-1 1sxi-6 2qq1-1 3d8u-d 4rkr-2 1sxg-1 1sxi-5 1sxh-d 4rkq-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP06143

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Molybdopterin adenylyltransferase

B: Molybdopterin adenylyltransferase

C: Molybdopterin adenylyltransferase

D: Molybdopterin adenylyltransferase

E: Molybdopterin adenylyltransferase

F: Molybdopterin adenylyltransferase

119 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Molybdopterin adenylyltransferase

B: Molybdopterin adenylyltransferase

C: Molybdopterin adenylyltransferase

defined by author&software
59.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Molybdopterin adenylyltransferase

E: Molybdopterin adenylyltransferase

F: Molybdopterin adenylyltransferase

defined by author&software
59.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.619, 66.018, 76.049
Angle α, β, γ (deg.)	71.97, 86.42, 60.22
Int Tables number	1
Space group name H-M	P1

#1: Protein	Molybdopterin adenylyltransferase / MPT adenylyltransferase Mass: 19844.090 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain J99 / ATCC 700824) (bacteria) Strain: J99 / ATCC 700824 / Gene: mog, mogA, jhp_0735 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9ZL45, molybdopterin adenylyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1157 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Molybdopterin adenylyltransferase / MPT adenylyltransferase

Mass: 19844.090 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Helicobacter pylori (strain J99 / ATCC 700824) (bacteria)
Strain: J99 / ATCC 700824 / Gene: mog, mogA, jhp_0735 / Plasmid: pMCSG53 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ZL45, molybdopterin adenylyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1157 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46 %
Crystal grow	Temperature: 310 K / Method: vapor diffusion, sitting drop Details: 25%PEG 3350. 0.2M calcium chloride dihydrate, 0.1 M Tris

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 31, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.8→25 Å / Num. obs: 91170 / % possible obs: 94.1 % / Redundancy: 3.1 % / R_merge(I) obs: 0.04 / Net I/σ(I): 36.98
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.596 / Mean I/σ(I) obs: 2.67 / % possible all: 90

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX	(phenix.phaser)	phasing
PHENIX	(phenix.autobuild)	model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2QQ1

2qq1

Resolution: 1.8→24.774 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 21.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1989	1916	2.18 %	Random selection
R_work	0.1637	-	-	-
obs	0.1644	87879	90.63 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→24.774 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8190	0	0	1157	9347

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	8438
X-RAY DIFFRACTION	f_angle_d	0.972	11422
X-RAY DIFFRACTION	f_dihedral_angle_d	12.458	3322
X-RAY DIFFRACTION	f_chiral_restr	0.037	1323
X-RAY DIFFRACTION	f_plane_restr	0.006	1470

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 (%)
1.8003-1.8453	0.2817	127	0.2461	5186	X-RAY DIFFRACTION	77
1.8453-1.8952	0.3108	120	0.2256	5510	X-RAY DIFFRACTION	81
1.8952-1.9509	0.2549	124	0.2089	5797	X-RAY DIFFRACTION	85
1.9509-2.0139	0.2576	125	0.1992	5801	X-RAY DIFFRACTION	87
2.0139-2.0858	0.216	131	0.1822	6037	X-RAY DIFFRACTION	89
2.0858-2.1693	0.21	142	0.1775	6121	X-RAY DIFFRACTION	90
2.1693-2.2679	0.2133	140	0.1678	6213	X-RAY DIFFRACTION	91
2.2679-2.3874	0.1845	139	0.1699	6239	X-RAY DIFFRACTION	93
2.3874-2.5369	0.2227	141	0.1802	6365	X-RAY DIFFRACTION	93
2.5369-2.7325	0.2273	138	0.1783	6413	X-RAY DIFFRACTION	95
2.7325-3.0071	0.2102	146	0.1805	6489	X-RAY DIFFRACTION	96
3.0071-3.4412	0.225	141	0.1668	6513	X-RAY DIFFRACTION	97
3.4412-4.3318	0.1638	156	0.1412	6603	X-RAY DIFFRACTION	98
4.3318-24.7766	0.1605	146	0.1361	6676	X-RAY DIFFRACTION	98

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	4.9304	-1.7313	0.0102	3.05	-2.202	4.1992	0.0756	-0.0553	-0.0989	0.2542	-0.057	-0.0239	-0.1607	-0.4985	-0.0304	0.1297	0.0591	0.0315	0.2774	0.0371	0.1739	-55.7167	58.0774	25.6353
2	6.7963	4.9398	2.3006	7.6078	3.6148	6.0798	0.0126	0.247	0.7205	-0.5279	-0.0661	0.6604	-0.7858	-0.3135	0.0728	0.2409	0.075	0.0185	0.2733	0.0294	0.2824	-54.7533	63.118	18.6569
3	3.2377	3.5647	3.5986	5.8419	3.0804	7.1004	0.0266	-0.4558	0.3089	0.4256	-0.1492	0.4133	-0.4764	-0.386	0.2367	0.3027	0.066	0.067	0.3629	0.0105	0.2833	-50.8388	62.9457	35.2364
4	3.0524	1.398	-0.3304	1.8295	0.1262	1.3022	-0.0528	0.0662	-0.037	-0.0385	0.0991	0.0004	-0.0415	-0.0469	-0.0453	0.2039	0.0105	-0.0119	0.2225	0.0269	0.2256	-41.1694	59.1674	24.2578
5	2.8341	-4.1109	-0.5491	7.5722	-1.3623	4.9391	0.0065	0.2861	-0.722	-0.8141	-0.0258	0.2223	0.5828	0.0699	-0.0668	0.3086	-0.0103	-0.0066	0.3247	-0.0676	0.4071	-49.1418	46.022	13.1215
6	5.6293	-1.5425	0.2604	7.5002	-2.4183	7.2601	-0.1017	0.0667	0.5791	0.1801	-0.1496	-0.6235	-0.281	0.7028	0.3068	0.2254	-0.1237	0.0137	0.2791	-0.0417	0.27	-12.0615	77.815	27.31
7	5.5299	-6.3459	6.8494	7.3235	-7.8135	8.5274	-0.9846	-0.6513	-0.3056	2.5076	0.0116	-1.5878	-0.1004	1.7932	0.9045	0.7857	0.0449	-0.0653	0.9498	0.1005	0.7657	2.1718	67.1567	23.6246
8	2.829	-1.0568	-0.1739	4.3953	-1.7864	6.5318	-0.0725	-0.1367	0.4037	0.1342	0.0136	-0.6734	-0.3285	0.5572	0.059	0.1929	-0.0705	-0.02	0.2414	-0.0372	0.3356	-12.1565	75.2842	29.0505
9	3.5071	-2.3542	0.1442	6.2729	1.2474	1.1806	0.0565	0.0137	-0.09	-0.112	-0.0507	-0.0916	-0.0505	0.0268	-0.0083	0.1576	-0.0082	0.0088	0.1541	0.0163	0.155	-19.3027	62.495	26.1943
10	2.447	-0.6468	-0.3335	4.775	0.2266	5.3049	0.1305	0.497	0.3298	-0.6468	-0.1013	-0.047	-0.2268	-0.1576	-0.0192	0.2612	-0.0307	-0.0094	0.2109	0.0527	0.1941	-22.2055	75.86	17.3086
11	9.569	-3.0225	-6.4656	3.3593	1.5805	8.4038	-0.57	-0.2993	-0.9425	0.292	0.229	-0.3418	0.489	0.4391	0.4372	0.3195	0.0691	0.037	0.2283	-0.0191	0.6859	-12.8809	33.2301	26.6797
12	5.9536	4.4721	-0.9285	6.0792	-2.3352	1.3933	0.5565	-1.1808	1.5463	-0.2895	0.3968	-0.5937	0.2586	-0.7284	-1.1247	0.8751	0.3329	0.0139	1.4457	0.1716	1.5092	-35.5937	25.8528	27.9321
13	5.6562	2.6248	-1.5881	3.572	-1.1717	5.3235	-0.3165	0.1288	-1.0696	0.0677	0.1345	0.2575	0.6337	-0.0948	0.1832	0.3762	0.0127	0.1074	0.2273	-0.0977	0.7024	-19.4114	30.7109	23.5776
14	5.6719	-0.5254	0.6731	2.4824	-0.6936	1.9501	-0.0795	-0.2136	-0.5426	0.153	0.1039	0.1409	0.1322	0.0194	-0.0353	0.197	0.0311	0.0282	0.1893	0.0054	0.2794	-25.4404	43.378	29.7526
15	3.6216	-0.4948	0.2448	3.3983	0.9271	4.4455	-0.0333	0.9176	-0.5847	-0.4343	0.0156	-0.0725	0.1723	0.1623	0.0251	0.2468	0.0314	0.0333	0.3117	-0.1008	0.3061	-15.1757	41.4824	17.9057
16	3.3196	1.52	1.7828	7.6811	-0.316	7.6496	-0.3697	-0.3486	0.3295	0.2776	0.2728	0.991	-0.1341	-1.2281	0.058	0.2376	-0.0887	-0.0428	0.4298	0.0307	0.4199	-71.3641	30.0803	60.8523
17	2.2643	-1.0099	-1.4035	5.6859	2.6818	3.3675	-0.0213	-0.1395	-0.3214	0.2394	-0.1169	0.6073	0.1948	-0.7711	0.202	0.2571	-0.0533	-0.0451	0.3513	0.0631	0.3337	-67.4067	29.3892	65.4479
18	2.2694	-1.1526	-0.2	6.195	-1.1724	0.9638	0.0601	0.0248	0.0071	-0.0974	-0.0638	0.038	0.0781	-0.0677	0.0115	0.2006	-0.0226	-0.037	0.2143	-0.0164	0.1824	-61.3071	42.9204	61.416
19	2.7935	-0.49	-0.0601	4.7591	-0.0582	3.0689	0.0558	0.1958	-0.2271	-0.4693	0.0198	0.1263	0.1537	-0.15	-0.0867	0.2243	-0.0458	-0.0201	0.1912	0.0055	0.2064	-59.1071	32.2412	57.4169
20	3.2699	1.5197	3.9862	2.4364	-0.2546	8.368	-0.4353	1.9079	-0.846	-0.7673	0.3887	-0.6847	0.5455	1.2029	-0.0216	0.6777	-0.001	0.1083	0.5819	-0.1115	0.4936	-51.1216	25.9677	48.5937
21	7.8154	-0.1437	0.8929	5.8413	0.0933	6.2971	-0.1592	-0.1358	0.9642	0.1235	-0.025	-0.1479	-0.4869	0.048	0.2585	0.2638	0.0382	0.0095	0.1368	0.019	0.2349	-61.7146	72.7477	63.3876
22	7.8787	7.2746	4.988	6.7059	4.5925	3.1651	0.5383	1.1374	2.6052	-0.9311	0.3286	-0.4318	-1.3741	-0.4736	-0.8617	1.0355	-0.0732	0.1416	0.9616	0.4595	1.2903	-45.9319	81.8464	59.6837
23	4.9104	-0.1828	2.6615	2.6661	-0.7021	7.1445	-0.1322	-0.197	0.5893	0.1435	-0.0313	-0.0582	-0.4399	-0.0168	0.1621	0.2562	0.0348	-0.0123	0.168	-0.0579	0.3163	-59.1533	72.023	64.8322
24	4.5702	-0.8515	-0.5116	1.522	0.6206	0.9677	0.1249	0.1286	0.1894	-0.126	-0.0693	-0.0029	-0.0134	-0.0387	-0.0517	0.2258	0.0239	-0.019	0.2107	0.0029	0.1825	-56.1722	61.0312	60.196
25	2.5399	2.2947	-1.0348	3.5573	-2.8747	3.0023	-0.2561	0.5101	0.1303	-0.9693	0.3393	0.4155	0.6873	-0.5761	-0.0923	0.4557	-0.0267	-0.0797	0.3819	-0.0072	0.3241	-70.8947	61.4752	48.3613
26	2.7791	-0.9017	-0.0954	9.0035	0.1109	6.4444	-0.0647	-0.6423	-1.2929	0.0565	-0.4245	-1.1409	0.7649	0.7086	0.0344	0.2687	0.0802	0.0495	0.3787	0.0456	0.877	-25.5528	42.6233	63.1589
27	3.7682	1.5976	-1.725	4.2114	0.3772	4.772	0.0745	-0.4304	-1.1617	0.3045	-0.223	-1.2789	0.3258	0.4845	0.1072	0.2514	0.0322	-0.0572	0.3115	0.0503	0.6905	-27.757	43.7189	65.6045
28	3.5266	2.8136	1.3215	7.0173	0.9287	1.9036	-0.0072	0.0076	-0.3654	-0.1305	0.1318	-0.3038	0.2001	0.0685	-0.0783	0.158	0.0068	0.0149	0.2125	0.021	0.2357	-43.7479	41.8413	61.2921
29	3.4744	1.5351	-0.8857	4.5813	0.2213	2.6977	-0.2385	0.2593	-0.3795	-0.5622	0.2154	-0.6986	0.1195	0.167	-0.014	0.2274	-0.025	0.0682	0.2279	-0.0483	0.3089	-32.3578	50.5964	57.0849
30	4.7197	-4.5728	0.4457	4.8631	-1.0786	3.5172	-0.0689	1.0522	1.1292	-1.9808	0.2731	-0.8937	-2.1404	-0.1816	-0.2008	0.7576	-0.0845	0.0384	0.4366	0.0383	0.5019	-33.9594	63.2537	51.2377

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid -1:19)
2	X-RAY DIFFRACTION	2	(chain A and resid 20:40)
3	X-RAY DIFFRACTION	3	(chain A and resid 41:66)
4	X-RAY DIFFRACTION	4	(chain A and resid 67:162)
5	X-RAY DIFFRACTION	5	(chain A and resid 163:176)
6	X-RAY DIFFRACTION	6	(chain B and resid -1:15)
7	X-RAY DIFFRACTION	7	(chain B and resid 16:23)
8	X-RAY DIFFRACTION	8	(chain B and resid 24:73)
9	X-RAY DIFFRACTION	9	(chain B and resid 74:131)
10	X-RAY DIFFRACTION	10	(chain B and resid 132:176)
11	X-RAY DIFFRACTION	11	(chain C and resid -1:12)
12	X-RAY DIFFRACTION	12	(chain C and resid 13:22)
13	X-RAY DIFFRACTION	13	(chain C and resid 23:49)
14	X-RAY DIFFRACTION	14	(chain C and resid 50:130)
15	X-RAY DIFFRACTION	15	(chain C and resid 131:175)
16	X-RAY DIFFRACTION	16	(chain D and resid -1:28)
17	X-RAY DIFFRACTION	17	(chain D and resid 29:66)
18	X-RAY DIFFRACTION	18	(chain D and resid 67:116)
19	X-RAY DIFFRACTION	19	(chain D and resid 117:166)
20	X-RAY DIFFRACTION	20	(chain D and resid 167:176)
21	X-RAY DIFFRACTION	21	(chain E and resid -1:15)
22	X-RAY DIFFRACTION	22	(chain E and resid 18:22)
23	X-RAY DIFFRACTION	23	(chain E and resid 23:66)
24	X-RAY DIFFRACTION	24	(chain E and resid 67:163)
25	X-RAY DIFFRACTION	25	(chain E and resid 164:176)
26	X-RAY DIFFRACTION	26	(chain F and resid -1:23)
27	X-RAY DIFFRACTION	27	(chain F and resid 24:74)
28	X-RAY DIFFRACTION	28	(chain F and resid 75:119)
29	X-RAY DIFFRACTION	29	(chain F and resid 120:169)
30	X-RAY DIFFRACTION	30	(chain F and resid 170:176)

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News

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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.

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