PDB-2qsi: Crystal structure of putative hydrogenase expression/formation pr...

ID or keywords:

Entry

Database: PDB / ID: 2qsi

Title

Crystal structure of putative hydrogenase expression/formation protein hupG from Rhodopseudomonas palustris CGA009

Components

Putative hydrogenase expression/formation protein hupG

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative hydrogenase expression/formation protein / hupG / MCSG / PSI-2 / SAD / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

[NiFe]-hydrogenase maturation factor HyaE / Hydrogenase-1 expression protein HyaE / Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology

Biological species

Rhodopseudomonas palustris (phototrophic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Nocek, B. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Structure of putative hydrogenase expression/formation protein hupG from Rhodopseudomonas palustris CGA009.
Authors: Nocek, B. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Jul 31, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 300

BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2qsi.cif.gz	65.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2qsi_validation.pdf.gz	463.1 KB	Display	wwPDB validaton report
Full document	2qsi_full_validation.pdf.gz	464.4 KB	Display
Data in XML	2qsi_validation.xml.gz	15.9 KB	Display
Data in CIF	2qsi_validation.cif.gz	21.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qs/2qsi ftp://data.pdbj.org/pub/pdb/validation_reports/qs/2qsi	HTTPS FTP

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Related structure data

Similar structure data	5jgj-d 5amt-d 3ljy-1 3aqg-3 4opw-2 3asf-1 3b5k-d 3572 5o2k-6 1b9k-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC6337

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#92 - Aug 2007 Anabolic Steroids similarity (1) #127 - Jul 2010 Crystallins similarity (1) #174 - Jun 2014 GFP-like Proteins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Putative hydrogenase expression/formation protein hupG

B: Putative hydrogenase expression/formation protein hupG

hetero molecules

29.3 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)	31.575, 41.126, 46.850
Angle α, β, γ (deg.)	107.72, 99.85, 101.75
Int Tables number	1
Space group name H-M	P1

Details

FPLS experiment indicated two forms of this protein: monomeric and dimeric. The dimeric form was crystallized and structure of dimer has been determined.

#1: Protein	Putative hydrogenase expression/formation protein hupG Mass: 14463.987 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: hupG, RPA0968 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6NB62
#2: Chemical	ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.9 Å³/Da / Density % sol: 35.23 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.5M Ammonium sulfate, 50mM MES pH 5.6, 2% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2007 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. all: 17173 / Num. obs: 17173 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / R_merge(I) obs: 0.058 / Net I/σ(I): 14.4
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.124 / Mean I/σ(I) obs: 7.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building
TLSMD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→30 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.936 / SU B: 4.339 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20133	877	5.1 %	RANDOM
R_work	0.15194	-	-	-
all	0.1565	17169	-	-
obs	0.15455	16292	87.16 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 13.359 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.35 Å²	-0.83 Å²	-0.56 Å²
2-	-	0.14 Å²	-0.67 Å²
3-	-	-	-0.73 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1676	0	22	233	1931

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1732
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1149
X-RAY DIFFRACTION	r_angle_refined_deg	1.6	1.978	2358
X-RAY DIFFRACTION	r_angle_other_deg	1	3.001	2801
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.765	5	224
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.149	24	70
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.529	15	261
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.381	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	285
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1925
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	341
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	339
X-RAY DIFFRACTION	r_nbd_other	0.204	0.2	1193
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	860
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	909
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	168
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.197	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.285	0.2	35
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.208	0.2	22
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.031	1.5	1349
X-RAY DIFFRACTION	r_mcbond_other	0.243	1.5	453
X-RAY DIFFRACTION	r_mcangle_it	1.247	2	1800
X-RAY DIFFRACTION	r_scbond_it	2.188	3	661
X-RAY DIFFRACTION	r_scangle_it	3.326	4.5	557
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.229	39	-
R_work	0.144	575	-
obs	-	-	42.08 %

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	3.097	1.6297	1.8137	5.7706	3.497	3.2826	0.1254	0.1436	-0.26	0.1086	0.4848	-0.7049	0.2437	0.5935	-0.6102	-0.0129	0.0425	-0.0443	0.0385	-0.0636	0.1111	-17.5805	-4.5201	-17.2149
2	3.3456	5.0796	1.5844	7.83	2.1039	1.5228	-0.0775	-0.0517	-0.0998	-0.0841	-0.0548	-0.0432	0.0433	0.11	0.1323	0.0339	-0.0015	0.0023	0.0588	0.0012	0.0406	-24.1452	1.9052	-18.5097
3	5.0146	-0.0767	1.9432	1.9028	-0.3383	3.7411	0.0157	-0.2654	-0.3331	0.1811	-0.057	0.1375	0.238	-0.2419	0.0413	0.0718	-0.0617	0.0442	0.051	-0.021	0.0614	-37.3445	-10.3053	-23.8568
4	16.0327	12.72	-2.5978	11.3662	-3.4976	2.8334	-0.1511	0.4308	0.5553	-0.1588	0.1509	0.5819	-0.0619	-0.1005	0.0002	0.0426	-0.0186	-0.0155	0.0317	0.006	0.0291	-34.4624	-0.8626	-27.8953
5	0.4438	-1.7926	-0.2721	8.5664	-1.7625	6.344	0.0217	0.1816	0.0369	0.3238	-0.0005	-0.0021	0.0677	-0.0561	-0.0212	0.09	-0.0489	-0.024	0.0287	0.0177	0.0028	-26.1514	7.9726	-27.986
6	1.3646	2.1202	0.3771	3.4176	-0.2582	5.8814	-0.2478	0.0791	0.222	0.0345	-0.0426	-0.1154	-0.1279	-0.0288	0.2904	0.0625	-0.0339	-0.0165	0.0506	0.0248	0.016	-21.9264	11.5171	-22.2135
7	2.4872	1.8551	-1.8627	1.8445	-0.4396	3.3526	-0.0043	0.1856	-0.0164	0.0914	-0.0081	-0.093	0.4149	0.2458	0.0125	0.0925	0.011	-0.0048	0.0244	-0.0157	0.0229	-25.62	-7.988	-20.7321
8	4.7659	-1.295	-1.7445	11.5858	8.7501	13.2477	0.2138	-0.1191	-0.18	0.8911	-0.3025	0.2363	1.0249	-0.2806	0.0887	0.1971	-0.0684	-0.0207	-0.0005	0.0188	-0.0583	-29.4593	-9.5107	-12.6568
9	3.4806	0.5494	2.3547	1.0111	2.0227	4.5417	0.0383	-0.236	0.034	0.2762	-0.1883	0.0809	0.2096	-0.4384	0.15	0.0699	-0.0427	0.0251	0.0629	-0.0088	-0.004	-31.8057	-2.7333	-13.7972
10	15.4023	0.8404	9.6292	0.0599	0.7537	9.7194	-0.3117	0.311	0.2674	-0.065	0.0626	0.1799	-0.2924	0.2916	0.2491	0.0758	0.001	-0.0258	0.0335	0.0127	0.0358	-19.7311	5.6297	-10.7467
11	9.9084	-0.7148	5.7955	0.7271	-1.0858	4.653	-0.1112	-0.1646	0.4116	-0.1827	-0.02	-0.0384	-0.2706	0.0917	0.1312	0.0351	-0.0075	-0.0058	0.038	0.0157	0.0484	-4.6347	10.0191	0.3631
12	10.6209	-12.1113	-3.2554	14.3978	2.7807	4.7422	-0.011	-0.2906	0.4873	-0.1781	0.2705	-0.6178	-0.3544	0.2415	-0.2594	0.0003	-0.0425	-0.0465	0.0269	-0.0285	0.0803	-3.0596	15.4683	11.5802
13	4.914	-1.604	4.1918	1.2392	-1.0094	8.0099	-0.097	-0.0214	0.0953	0.0342	-0.1027	-0.0087	-0.1863	-0.0299	0.1997	0.0344	-0.0107	-0.0053	-0.0054	0.0128	0.06	-9.0851	16.7137	5.1045
14	17.0557	-1.7211	3.9186	24.5717	-6.6315	12.9699	0.3566	1.3848	0.7574	-0.5003	-0.2868	-0.0448	-0.787	0.3355	-0.0697	0.0331	0.0551	-0.0376	0.1059	0.106	0.0393	-17.8753	19.8136	-4.2507
15	3.197	-1.0364	1.5376	0.734	1.0886	7.0686	0.0958	-0.1092	-0.0643	-0.0037	-0.042	0.0986	0.0544	-0.24	-0.0538	0.0077	-0.0136	0.004	0.0275	0.0167	0.0619	-12.5479	-5.9428	4.9726
16	11.7762	-6.2226	1.1729	3.9442	-0.4911	1.5007	-0.2808	-0.3167	0.1413	-0.0235	0.2385	-0.1421	0.1019	-0.0672	0.0423	0.0286	-0.0003	-0.0052	0.0558	0.0139	0.0419	-20.3409	-2.3837	1.0436
17	2.6251	-2.162	0.5855	1.7912	-0.4882	0.1339	-0.0267	0.0274	-0.0107	-0.0566	-0.0788	-0.0167	0.0491	-0.0517	0.1055	0.0165	-0.0154	0.0086	0.0854	-0.0064	0.0534	-15.1744	5.3851	3.913
18	1.243	-0.3017	1.0709	1.5115	0.0631	2.7637	0.054	0.0313	-0.1903	-0.0431	-0.0584	-0.0879	0.1019	0.1474	0.0044	0.0204	-0.0112	-0.0013	0.0619	0.0349	0.0551	2.6562	-1.4579	8.5652
19	20.3747	-8.2481	-0.8401	5.8539	0.7408	4.3727	-0.0947	-0.2333	0.199	0.2081	0.0915	-0.1991	-0.1695	0.2047	0.0032	0.0445	-0.0175	-0.0081	0.0238	0.013	0.0309	0.8327	4.8119	13.3087
20	15.1734	-9.2783	-6.3564	7.2356	1.4168	6.5686	-0.009	-0.2222	0.1634	0.2076	0.0131	-0.0645	-0.0628	0.1798	-0.0041	0.045	-0.0034	0.0088	0.0138	-0.0202	0.0582	-8.9426	7.9475	15.003
21	1.4173	1.1991	-0.0508	3.3561	2.4441	2.6433	0.0485	-0.0348	-0.009	0.0482	-0.1998	0.0512	0.0396	0.0462	0.1513	0.0147	0.0004	0.0035	0.0578	-0.02	0.0471	-17.2648	12.0102	9.2277
22	7.1554	-4.469	-5.2281	4.0374	3.8427	4.0874	0.1438	0.0626	-0.0377	-0.1091	-0.2184	0.2049	0.1476	0.0795	0.0746	0.027	0.0044	0.0014	0.0502	0.016	0.0548	-7.8736	-4.1032	6.3244
23	2.3639	0.6474	1.6073	2.7087	-2.308	5.1392	0.0922	0.043	0.0069	-0.1238	-0.163	-0.0818	0.1199	0.1745	0.0708	0.0318	0.0216	0.0033	0.0633	-0.0025	0.019	-5.4607	-2.9202	-2.7457
24	0.2689	0.2356	0.6713	0.871	0.274	1.8247	-0.0169	0.028	-0.0787	0.0158	-0.0309	0.0626	-0.0122	0.101	0.0478	0.0189	-0.0077	0.0036	0.0977	0.0153	0.0287	-2.8553	5.2613	1.6543
25	16.8276	8.4642	9.9216	4.5154	5.9515	9.4296	-0.1824	-0.0666	0.7394	0.1055	-0.1371	0.1558	0.1431	-0.1442	0.3195	0.0509	0.0184	-0.0017	0.06	-0.0203	0.0201	-18.9866	5.7845	-5.0984
26	0.2661	0.7672	0.0949	4.3736	-1.1855	1.0185	-0.1883	-0.0554	0.0034	-0.1155	0.1381	0.3396	-0.0013	-0.2301	0.0501	-0.0257	0.0154	-0.016	0.1649	-0.0563	0.0241	-35.0925	5.2915	-19.1066
27	6.0276	3.2781	4.6267	1.7865	2.3887	7.9516	-0.0036	0.2145	0.1328	0.0438	-0.0696	0.2607	-0.2655	-0.0474	0.0731	0.048	0.0602	-0.0375	0.0463	-0.0169	0.0232	-32.2237	11.9256	-19.1885
28	19.2237	7.4576	5.6421	12.4009	0.1228	32.5538	0.0738	-0.7912	0.6403	0.3909	-0.4103	0.4524	-1.1799	-0.1059	0.3366	0.1353	-0.0078	-0.0699	-0.0475	-0.0919	0.0201	-24.5437	18.0831	-9.9928

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	15 - 30	17 - 32
2	X-RAY DIFFRACTION	2	A	A	31 - 38	33 - 40
3	X-RAY DIFFRACTION	3	A	A	39 - 45	41 - 47
4	X-RAY DIFFRACTION	4	A	A	46 - 55	48 - 57
5	X-RAY DIFFRACTION	5	A	A	56 - 60	58 - 62
6	X-RAY DIFFRACTION	6	A	A	61 - 67	63 - 69
7	X-RAY DIFFRACTION	7	A	A	68 - 74	70 - 76
8	X-RAY DIFFRACTION	8	A	A	75 - 81	77 - 83
9	X-RAY DIFFRACTION	9	A	A	82 - 91	84 - 93
10	X-RAY DIFFRACTION	10	A	A	92 - 98	94 - 100
11	X-RAY DIFFRACTION	11	A	A	99 - 105	101 - 107
12	X-RAY DIFFRACTION	12	A	A	106 - 110	108 - 112
13	X-RAY DIFFRACTION	13	A	A	111 - 120	113 - 122
14	X-RAY DIFFRACTION	14	A	A	121 - 126	123 - 128
15	X-RAY DIFFRACTION	15	B	B	15 - 22	17 - 24
16	X-RAY DIFFRACTION	16	B	B	23 - 29	25 - 31
17	X-RAY DIFFRACTION	17	B	B	30 - 37	32 - 39
18	X-RAY DIFFRACTION	18	B	B	38 - 45	40 - 47
19	X-RAY DIFFRACTION	19	B	B	46 - 51	48 - 53
20	X-RAY DIFFRACTION	20	B	B	52 - 57	54 - 59
21	X-RAY DIFFRACTION	21	B	B	58 - 67	60 - 69
22	X-RAY DIFFRACTION	22	B	B	68 - 74	70 - 76
23	X-RAY DIFFRACTION	23	B	B	75 - 83	77 - 85
24	X-RAY DIFFRACTION	24	B	B	84 - 93	86 - 95
25	X-RAY DIFFRACTION	25	B	B	94 - 98	96 - 100
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