PDB-3kwl: Crystal structure of a hypothetical protein from Helicobacter pylori

ID or keywords:

Entry

Database: PDB / ID: 3kwl

Title

Crystal structure of a hypothetical protein from Helicobacter pylori

Components

uncharacterized protein

Keywords

UNKNOWN FUNCTION / putative oxidoreductase / multidomain

Function / homology

Function and homology information

Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 - #20 / Rossmann fold - #11810 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Beta-grasp domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Ubiquitin-like (UB roll) / Roll / Up-down Bundle / Rossmann fold ...
Similarity search - Domain/homology

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.94 Å

Authors

Lam, R. / Thompson, C.M. / Vodsedalek, J. / Lam, K. / Romanov, V. / Battaile, K.P. / Beletskaya, I. / Gordon, E. / Pai, E.F. / Chirgadze, N.Y.

Citation

Journal: To be Published
Title: Crystal structure of a hypothetical protein from Helicobacter pylori
Authors: Lam, R. / Thompson, C.M. / Vodsedalek, J. / Lam, K. / Romanov, V. / Battaile, K.P. / Beletskaya, I. / Gordon, E. / Pai, E.F. / Chirgadze, N.Y.

History

Deposition	Dec 1, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 1, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 30, 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 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.db_align_beg / _struct_ref_seq.db_align_end

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kwl.cif.gz	121.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3kwl.ent.gz	91.3 KB	Display	PDB format
PDBx/mmJSON format	3kwl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3kwl_validation.pdf.gz	416.7 KB	Display	wwPDB validaton report
Full document	3kwl_full_validation.pdf.gz	417.9 KB	Display
Data in XML	3kwl_validation.xml.gz	23.8 KB	Display
Data in CIF	3kwl_validation.cif.gz	33.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kw/3kwl ftp://data.pdbj.org/pub/pdb/validation_reports/kw/3kwl	HTTPS FTP

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Related structure data

Similar structure data	2j7u-d 1xf5-1 2vsf-d 3fzh-d 7cgq-2 5k5m-d 6lw4-d 5aqt-d 5aqh-d 6ecp-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: uncharacterized protein

60.1 kDa, 1 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)	47.623, 95.099, 65.048
Angle α, β, γ (deg.)	90.000, 109.140, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

The protein is monomeric with one molecule in the asymmetric unit.

#1: Protein	uncharacterized protein Mass: 60115.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HPAG1_0444 / Plasmid: pW2 (based on pET15B) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIPL
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.31 Å³/Da / Density % sol: 46.86 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 22% PEG3350, 0.2M MgCl2, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-BM / Wavelength: 0.9796 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2008 / Details: Si(111) double-crystal monochromator

Radiation

Monochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9796 Å / Relative weight: 1

Reflection

Resolution: 1.94→50 Å / Num. obs: 39957 / % possible obs: 99.5 % / Redundancy: 7.3 % / R_merge(I) obs: 0.091 / Χ²: 1.288 / Net I/σ(I): 10.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
1.95-2.02	5.9	0.426	3874	0.915	96
2.02-2.1	6.8	0.347	3976	0.948	99.4
2.1-2.2	7.3	0.279	3977	0.99	100
2.2-2.31	7.5	0.22	4018	1.087	100
2.31-2.46	7.6	0.166	3965	1.142	100
2.46-2.65	7.6	0.128	4036	1.18	100
2.65-2.91	7.7	0.101	3975	1.279	100
2.91-3.33	7.7	0.075	4035	1.244	100
3.33-4.2	7.6	0.061	4022	1.452	100
4.2-50	7.5	0.067	4079	2.485	99.7

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Phasing

Phasing

Method:

SAD

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	1.94	30.73	38731	1191
ANO_1	0.795	0	1.94	30.73	38439	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	Reflection acentric	Reflection centric
ISO_1	8.38-30.73	0	454	58
ISO_1	6.04-8.38	0	797	60
ISO_1	4.96-6.04	0	1038	65
ISO_1	4.31-4.96	0	1206	59
ISO_1	3.87-4.31	0	1385	59
ISO_1	3.53-3.87	0	1528	60
ISO_1	3.27-3.53	0	1681	63
ISO_1	3.06-3.27	0	1779	60
ISO_1	2.89-3.06	0	1910	60
ISO_1	2.74-2.89	0	2022	60
ISO_1	2.62-2.74	0	2114	62
ISO_1	2.51-2.62	0	2185	54
ISO_1	2.41-2.51	0	2340	62
ISO_1	2.32-2.41	0	2408	62
ISO_1	2.24-2.32	0	2479	61
ISO_1	2.17-2.24	0	2568	59
ISO_1	2.11-2.17	0	2696	64
ISO_1	2.05-2.11	0	2705	62
ISO_1	1.99-2.05	0	2782	54
ISO_1	1.94-1.99	0	2654	47
ANO_1	8.38-30.73	0.442	443	0
ANO_1	6.04-8.38	0.379	797	0
ANO_1	4.96-6.04	0.401	1038	0
ANO_1	4.31-4.96	0.5	1206	0
ANO_1	3.87-4.31	0.54	1385	0
ANO_1	3.53-3.87	0.577	1528	0
ANO_1	3.27-3.53	0.626	1681	0
ANO_1	3.06-3.27	0.665	1779	0
ANO_1	2.89-3.06	0.704	1910	0
ANO_1	2.74-2.89	0.743	2022	0
ANO_1	2.62-2.74	0.795	2114	0
ANO_1	2.51-2.62	0.843	2185	0
ANO_1	2.41-2.51	0.882	2340	0
ANO_1	2.32-2.41	0.909	2408	0
ANO_1	2.24-2.32	0.937	2479	0
ANO_1	2.17-2.24	0.958	2567	0
ANO_1	2.11-2.17	0.974	2695	0
ANO_1	2.05-2.11	0.978	2684	0
ANO_1	1.99-2.05	0.986	2696	0
ANO_1	1.94-1.99	0.993	2482	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	4.21	36.328	14.733	SE	27.42	1.1
2	-12.99	65.362	13.815	SE	34.38	1.13
3	-3.377	60.45	13.21	SE	34.15	1.01
4	-4.613	32.138	15.263	SE	37.74	0.88
5	-9.996	56.478	-1.245	SE	41.89	0.93
6	7.801	33.473	25.816	SE	22.55	0.68
7	2.202	45.222	-10.212	SE	25.74	0.69
8	-15.208	69.199	16.475	SE	38.58	0.89

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 39922

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.44-100	61.3	0.821	505
6.59-8.44	59.4	0.901	555
5.59-6.59	55.3	0.903	674
4.94-5.59	56.4	0.928	783
4.47-4.94	56.2	0.935	849
4.11-4.47	58.3	0.942	938
3.83-4.11	60.3	0.924	1014
3.6-3.83	60.4	0.91	1082
3.41-3.6	61.3	0.912	1127
3.24-3.41	62.2	0.904	1218
3.1-3.24	59.7	0.884	1272
2.97-3.1	60.9	0.882	1306
2.86-2.97	64.3	0.852	1383
2.76-2.86	66.9	0.863	1426
2.67-2.76	65.2	0.876	1455
2.59-2.67	67.3	0.872	1511
2.51-2.59	68.7	0.868	1568
2.45-2.51	72.2	0.867	1625
2.38-2.45	70.7	0.878	1625
2.32-2.38	72.3	0.873	1708
2.27-2.32	77.7	0.876	1718
2.22-2.27	73.7	0.881	1788
2.17-2.22	77	0.886	1794
2.13-2.17	79.6	0.872	1888
2.08-2.13	82.1	0.871	1875
2.04-2.08	79.5	0.857	1919
2.01-2.04	81.8	0.83	1941
1.94-2.01	84.2	0.772	3375

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.5.0102	refinement
PDB_EXTRACT	3.005	data extraction
JDirector		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.94→30.73 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.217 / WR_factor R_work: 0.176 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 8.2 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.219	1994	5 %	RANDOM
R_work	0.179	-	-	-
obs	0.181	39919	99.18 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 51.72 Å² / B_iso mean: 22.662 Å² / B_iso min: 9.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.06 Å²	0 Å²	-0.05 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.94→30.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4100	0	0	274	4374

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4224
X-RAY DIFFRACTION	r_angle_refined_deg	1.183	1.964	5720
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.75	5	503
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.232	25.263	209
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.227	15	757
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.111	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	615
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3208
X-RAY DIFFRACTION	r_mcbond_it	0.614	1.5	2501
X-RAY DIFFRACTION	r_mcangle_it	1.198	2	4041
X-RAY DIFFRACTION	r_scbond_it	1.978	3	1723
X-RAY DIFFRACTION	r_scangle_it	3.246	4.5	1676

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.945-1.995	0.323	138	0.24	2598	3001	91.17
1.995-2.05	0.258	136	0.21	2689	2873	98.329
2.05-2.109	0.245	118	0.204	2653	2778	99.748
2.109-2.173	0.258	138	0.2	2616	2754	100
2.173-2.244	0.244	135	0.189	2494	2629	100
2.244-2.323	0.236	128	0.187	2410	2538	100
2.323-2.41	0.227	125	0.184	2343	2468	100
2.41-2.508	0.254	139	0.195	2259	2400	99.917
2.508-2.618	0.204	98	0.186	2140	2238	100
2.618-2.745	0.249	113	0.195	2064	2179	99.908
2.745-2.892	0.251	125	0.198	1947	2073	99.952
2.892-3.066	0.264	90	0.198	1882	1972	100
3.066-3.275	0.207	85	0.181	1755	1840	100
3.275-3.535	0.194	91	0.163	1648	1739	100
3.535-3.867	0.171	73	0.158	1510	1583	100
3.867-4.315	0.187	69	0.152	1376	1446	99.931
4.315-4.966	0.183	83	0.145	1186	1271	99.843
4.966-6.043	0.175	54	0.181	1042	1096	100
6.043-8.385	0.218	38	0.169	819	857	100
8.385-30.726	0.194	18	0.148	494	514	99.611

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	0.5388	-0.4944	-0.124	1.3303	0.6992	0.5316	0.0755	0.0587	0.0307	-0.1454	-0.1083	-0.0225	-0.0944	-0.0123	0.0328	0.0607	0.0383	0.0116	0.0718	0.0173	0.0264	12.957	16.388	10.81
2	7.3484	-1.6007	-0.9016	7.1665	2.8194	2.6344	-0.0378	-0.0023	0.2714	-0.5454	-0.0552	0.16	-0.4166	0.1252	0.093	0.1094	0.0009	-0.0487	0.024	0.0052	0.0771	7.313	39.199	22.806
3	0.4597	-0.1703	0.2126	1.1181	0.117	0.4678	0.0007	-0.0245	0.0074	-0.0033	0.0196	-0.0003	0.0582	0.0311	-0.0203	0.0431	0.0035	0.0272	0.0435	-0.0023	0.0304	24.896	26.958	39.171

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 194
2	X-RAY DIFFRACTION	2	A	195 - 205
3	X-RAY DIFFRACTION	3	A	206 - 495

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