PDB-2xuv: The structure of HdeB

ID or keywords:

Entry

Database: PDB / ID: 2xuv

Title

The structure of HdeB

Components

HDEB

Keywords

UNKNOWN FUNCTION

Function / homology

Function and homology information

cellular stress response to acidic pH / response to acidic pH / unfolded protein binding / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.5 Å

Authors

Naismith, J.H. / Wang, W.

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Salt Bridges Regulate Both Dimer Formation and Monomeric Flexibility in Hdeb and May Have a Role in Periplasmic Chaperone Function.
Authors: Wang, W. / Rasmussen, T. / Harding, A.J. / Booth, N.A. / Booth, I.R. / Naismith, J.H.

History

Deposition	Oct 21, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 24, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 21, 2011	Group: Database references
Revision 1.2	Nov 30, 2011	Group: Database references
Revision 1.3	Dec 21, 2011	Group: Database references
Revision 1.4	Jan 25, 2012	Group: Other

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xuv.cif.gz	134.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2xuv.ent.gz	116.2 KB	Display	PDB format
PDBx/mmJSON format	2xuv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xu/2xuv ftp://data.pdbj.org/pub/pdb/validation_reports/xu/2xuv	HTTPS FTP

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Related structure data

Similar structure data	4mi8-1 2x4y-3 4d5t-1 2i6o-d 6udx-1 2kkn-d 1yzt-2 2z2d-d 3wiy-2 2vog-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: HDEB

B: HDEB

C: HDEB

D: HDEB

hetero molecules

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

1

A: HDEB

B: HDEB

hetero molecules

defined by author&software
18.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: HDEB

D: HDEB

hetero molecules

defined by author&software
18.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.920, 86.500, 48.500
Angle α, β, γ (deg.)	90.00, 112.54, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	HDEB / 10K-L PROTEIN Mass: 9290.586 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AET2
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE PERIPLASMIC LEADER SEQUENCE IS CLEAVED OFF DURING SYNTHESIS. HDEB IS FOUND IN THE PERIPLASM. ...THE PERIPLASMIC LEADER SEQUENCE IS CLEAVED OFF DURING SYNTHESIS. HDEB IS FOUND IN THE PERIPLASM. MNISSLRKAFIFMGAVAALSLVNAQSALA

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.24 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 1.5→33 Å / Num. obs: 58562 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / B_iso Wilson estimate: 19 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 2.7
Reflection shell	Resolution: 1.5→1.54 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.21 / Mean I/σ(I) obs: 2.7 / % possible all: 94.5

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0086	refinement
MOSFLM		data reduction
SCALA		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.5→32.78 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.951 / SU B: 2.03 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TYR 64 IN THE A SUBUNIT AND TO SOME EXTENT IN THE B SUBUNIT SHOWS EVIDENCE OF METHYLATION.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19544	2943	5 %	RANDOM
R_work	0.18149	-	-	-
obs	0.18218	55610	95.26 %	-

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 mean: 18.701 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	-0.04 Å²
2-	-	-0.06 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→32.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2305	0	10	268	2583

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	2516
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1641
X-RAY DIFFRACTION	r_angle_refined_deg	1.346	1.988	3457
X-RAY DIFFRACTION	r_angle_other_deg	0.902	3	4106
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.269	5	315
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.109	27.094	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.49	15	415
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	394
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2727
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	429
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.228	205	-
R_work	0.193	4060	-
obs	-	-	94.53 %

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	3.2859	0.2945	-2.1102	4.0487	1.9895	5.9203	-0.0321	-0.1222	0.0665	0.2639	-0.0025	-0.0838	0.2647	0.0833	0.0346	0.042	-0.0043	-0.0133	0.0139	-0.0049	0.0193	-30.028	-5.095	-8.618
2	8.5883	2.7778	-2.525	4.3926	-0.036	2.925	-0.0135	0.0078	-0.1685	0.0347	0.0099	0.1554	0.0772	-0.2454	0.0036	0.0175	-0.0052	-0.0075	0.0386	0.0089	0.0239	-39.855	-15.074	-10.549
3	3.4694	-2.4262	1.5403	4.6372	-2.3442	2.1836	0.1304	0.0593	-0.156	-0.1254	-0.0679	0.3193	0.1333	-0.1438	-0.0625	0.0773	-0.0209	-0.0265	0.0934	0.001	0.0478	-43.471	-17.863	-19.138
4	3.7492	2.5782	1.4857	5.271	1.5009	3.4871	-0.0287	-0.1006	0.3296	0.0317	-0.0667	0.5228	-0.0976	-0.139	0.0953	0.0187	0.0219	0.0074	0.0469	-0.0301	0.1178	-40.38	-1.251	-9.954
5	2.1793	0.2062	-0.7599	2.7952	0.1331	2.1813	0.0499	0.0295	0.0542	-0.1202	-0.0209	-0.2175	-0.0414	0.0495	-0.029	0.0264	0.0089	0.0101	0.0199	0.0012	0.0195	-25.624	-13.81	-14.234
6	7.0148	-0.8298	-2.5439	3.4579	2.3295	4.4854	-0.1841	0.1613	-0.5186	-0.0942	0.0297	0.2251	0.4909	-0.4277	0.1544	0.1605	-0.0412	-0.0281	0.1268	0.0211	0.1219	-38.58	-25.591	-11.564
7	7.3896	3.4192	-5.3915	2.5658	-2.8149	5.8118	-0.0247	-0.4012	-0.3133	-0.0859	-0.1733	-0.339	0.1725	0.4994	0.1979	0.063	0.0332	0.0122	0.0953	0.0174	0.0689	-22.079	-23.503	-7.585
8	8.5583	-3.0936	-0.502	6.5388	-0.8538	7.5617	0.0146	0.3022	-0.3233	-0.5289	-0.0112	-0.2032	0.4936	0.3031	-0.0034	0.1524	0.0389	0.0564	0.0875	-0.0241	0.0706	-21.104	-22.576	-18.526
9	3.4586	2.1336	0.3693	4.5606	0.1467	1.5347	-0.0277	0.2234	0.0797	-0.2798	0.0127	0.2585	-0.0222	-0.0114	0.0149	0.0679	-0.0123	-0.0213	0.0498	-0.0062	0.0168	-23.965	12.833	-12.783
10	9.118	-0.4567	8.5452	20.3249	-14.2355	17.4088	-1.5258	0.2115	0.9085	1.115	-0.0663	-1.1406	-2.229	0.2611	1.5922	0.8112	-0.1935	0.0076	0.3549	0.0274	0.2625	-10.84	24.748	-10.205
11	3.669	1.995	2.4883	2.898	1.8124	4.1331	-0.1051	-0.1425	0.3433	-0.2454	-0.1252	0.6019	-0.193	-0.34	0.2303	0.0911	0.0204	-0.0519	0.0847	0.0029	0.1507	-28.53	20.396	-9.14
12	16.1326	1.4427	16.6349	10.5704	-1.7286	46.2839	-0.6755	0.5886	1.9443	-0.7406	0.2817	0.3956	-2.8711	0.1122	0.3937	0.4137	-0.0065	-0.1189	0.1205	0.1053	0.4935	-27.919	25.365	-15.81
13	1.9242	1.8096	0.1396	4.5566	-0.1672	1.0195	0.0168	0.0254	-0.1191	0.0195	0.0009	-0.0887	-0.0215	0.0468	-0.0177	0.0339	-0.0137	-0.0002	0.0502	-0.0168	0.0275	-17.369	6.221	-9.549
14	2.0051	-0.5838	3.2325	9.4079	0.0221	5.3171	0.0894	0.3708	0.1218	-0.6228	-0.2097	-0.8484	0.0621	0.6193	0.1203	0.0932	-0.0473	0.0823	0.2832	0.0253	0.1671	-6.099	16.851	-13.273
15	8.0385	2.184	-3.7863	7.7806	-0.4229	7.561	0.171	0.4978	-0.3398	-0.3063	0.0013	-0.8142	-0.0993	0.1037	-0.1723	0.0349	0.0119	0.0278	0.1419	-0.0206	0.2003	-10.342	-2.411	-12.107
16	5.3977	0.8889	-1.5662	11.5618	-0.1967	8.6049	0.2287	-0.234	-0.1104	0.4459	-0.1052	-1.3121	0.0467	0.6201	-0.1235	0.0428	-0.0182	-0.0742	0.1442	0.012	0.256	-7.826	2.726	-5.121

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	32 - 48
2	X-RAY DIFFRACTION	2	A	49 - 66
3	X-RAY DIFFRACTION	3	A	67 - 77
4	X-RAY DIFFRACTION	4	A	78 - 100
5	X-RAY DIFFRACTION	5	B	30 - 57
6	X-RAY DIFFRACTION	6	B	58 - 71
7	X-RAY DIFFRACTION	7	B	72 - 91
8	X-RAY DIFFRACTION	8	B	92 - 100
9	X-RAY DIFFRACTION	9	C	32 - 59
10	X-RAY DIFFRACTION	10	C	60 - 70
11	X-RAY DIFFRACTION	11	C	71 - 96
12	X-RAY DIFFRACTION	12	C	97 - 101
13	X-RAY DIFFRACTION	13	D	32 - 59
14	X-RAY DIFFRACTION	14	D	60 - 78
15	X-RAY DIFFRACTION	15	D	79 - 93
16	X-RAY DIFFRACTION	16	D	94 - 101

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