PDB-4aq1: Structure of the SbsB S-layer protein of Geobacillus stearothermo...

ID or keywords:

Entry

Database: PDB / ID: 4aq1

Title

Structure of the SbsB S-layer protein of Geobacillus stearothermophilus PV72p2 in complex with nanobody KB6

Components

(SBSB PROTEIN) x 2
NBKB6

Keywords

STRUCTURAL PROTEIN /

S-LAYER PROTEIN /

NANOBODY

Function / homology

Function and homology information

identical protein binding /

metal ion binding
Similarity search - Function

Biological species

GEOBACILLUS STEAROTHERMOPHILUS (bacteria)

LAMA GLAMA (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.42 Å

Authors

Baranova, E. / Remaut, H.

Citation

Journal: Nature / Year: 2012
Title: Sbsb Structure and Lattice Reconstruction Unveil Ca21 Triggered S-Layer Assembly
Authors: Baranova, E. / Fronzes, R. / Garcia-Pino, A. / Van Gerven, N. / Papapostolou, D. / Pehau-Arnaudet, G. / Pardon, E. / Steyaert, J. / Howorka, S. / Remaut, H.

History

Deposition	Apr 12, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 11, 2012	Group: Other
Revision 1.2	Oct 3, 2012	Group: Derived calculations

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4aq1.cif.gz	610.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4aq1.ent.gz	512.7 KB	Display	PDB format
PDBx/mmJSON format	4aq1.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/aq/4aq1 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aq1	HTTPS FTP

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Related structure data

Similar structure data	1bgw-d 2q5g-3 4tkz-d 5ejs-d 6jp9-d 3guw-d 6was-d 5ocr-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: SBSB PROTEIN

B: NBKB6

C: SBSB PROTEIN

D: NBKB6

hetero molecules

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

1

A: SBSB PROTEIN

hetero molecules

B: NBKB6

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

2

B: NBKB6

A: SBSB PROTEIN

hetero molecules

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

3

C: SBSB PROTEIN

hetero molecules

D: NBKB6

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

4

D: NBKB6

C: SBSB PROTEIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.500, 88.500, 95.200
Angle α, β, γ (deg.)	112.50, 101.60, 84.70
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
1	2	B
2	2	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	295 - 920
2	1	1	4	C	295 - 920
1	1	2	4	B	1 - 124
2	1	2	4	D	1 - 124

NCS ensembles :

ID
1
2

#1: Protein	SBSB PROTEIN Mass: 94961.180 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-920 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Strain: PV72P2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / Variant (production host): PLYSS / References: UniProt: Q45664
#2: Antibody	NBKB6 Mass: 13992.331 Da / Num. of mol.: 2 / Fragment: VHH Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WK6
#3: Protein	SBSB PROTEIN Mass: 94975.203 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-920 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Strain: PV72P2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / Variant (production host): PLYSS / References: UniProt: Q45664
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	CHAINS B, D RESIDUES 125-130 IS HEXA-HIS EXPRESSION TAG.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.3 % / Description: NONE
Crystal grow	pH: 6.5 Details: 0.2 M KSCN, 0.1 M BIS-TRIS PROPANE PH 6.5 AND 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.8726
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.4→58.5 Å / Num. obs: 74487 / % possible obs: 97.9 % / Redundancy: 4 % / R_merge(I) obs: 0.11 / Net I/σ(I): 11
Reflection shell	Resolution: 2.4→2.5 Å / Redundancy: 4 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2.5 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.42→43.81 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.917 / SU B: 14.587 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23567	3729	5 %	RANDOM
R_work	0.18301	-	-	-
obs	0.18565	70750	97.05 %	-

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: 31.829 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0.02 Å²	-0.05 Å²
2-	-	0.24 Å²	-0.07 Å²
3-	-	-	-0.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.42→43.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11852	0	8	475	12335

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.02	11881
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7487
X-RAY DIFFRACTION	r_angle_refined_deg	1.491	1.949	16196
X-RAY DIFFRACTION	r_angle_other_deg	0.902	3	18530
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.862	5	1590
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.423	26.753	465
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.991	15	1909
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.088	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1996
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	13445
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2127
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

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	7501	medium positional	0.44	0.5
2	C	7501	medium positional	0.44	0.5
1	B	1512	medium positional	0.34	0.5
1	D	1512	medium positional	0.34	0.5
1	A	7501	medium thermal	2.84	2
2	C	7501	medium thermal	2.84	2
1	B	1512	medium thermal	5.94	2
1	D	1512	medium thermal	5.94	2

LS refinement shell

Resolution: 2.424→2.487 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	227	-
R_work	0.294	4602	-
obs	-	-	85.56 %

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	1.868	4.2852	1.0613	10.2201	3.0609	4.6578	-0.1692	0.0231	0.5955	0.8835	-0.1757	1.4752	-0.3723	-0.2187	0.3449	0.683	0.254	0.1164	0.4463	-0.0827	0.2765	1.315	-48.593	26.515
2	2.684	-2.1856	2.1847	6.3546	0.3758	2.7954	-0.1846	-0.5213	-0.4535	0.2156	0.4289	0.6452	-0.1282	-0.4401	-0.2442	0.0922	0.0257	0.0308	0.2123	0.1567	0.1983	1.207	-54.576	17.39
3	0.7826	-1.7783	0.9096	39.5555	-1.4783	1.0675	-0.1963	-0.1281	0.11	0.1096	0.0546	0.0209	-0.2316	-0.1507	0.1417	0.1436	0.0491	0.0114	0.0487	0.0113	0.1174	7.348	-44.22	14.618
4	2.8353	1.5862	0.3645	7.6242	0.6139	3.3223	0.0145	-0.2205	0.0482	0.2752	0.1031	-0.4745	0.0925	0.2106	-0.1176	0.0565	0.0051	-0.0459	0.0427	-0.0167	0.0917	12.446	-56.629	16.664
5	1.752	-0.5947	1.0459	3.5913	1.0408	4.1534	-0.0337	-0.2169	-0.0169	0.3569	0.0623	0.0526	-0.1861	-0.2962	-0.0286	0.1202	-0.0037	0.021	0.0703	0.0343	0.0575	5.381	-51.457	19.778
6	0.2203	0.4108	0.2589	2.1977	0.7409	0.5206	0.003	0.0273	0.0098	0.0755	-0.1128	0.4242	0.0254	-0.1394	0.1097	0.1139	-0.0002	0.0724	0.1481	-0.0474	0.164	-22.166	-20.15	2.674
7	2.0883	-0.7343	1.5569	1.5989	-1.0874	1.8724	0.0967	0.1625	-0.1205	-0.0707	-0.0677	-0.169	0.0616	0.1058	-0.029	0.0192	0.0032	-0.0096	0.0162	-0.0053	0.1147	24.062	20.319	6.249
8	0.796	-0.0214	0.3017	1.1528	-0.4003	0.4155	0.0144	0.0076	-0.0858	0.007	-0.0087	-0.1894	0.0683	0.0055	-0.0057	0.1052	0.002	0.0307	0.0253	-0.0213	0.099	-0.354	-16.579	3.204
9	1.308	-0.4491	0.3765	1.3143	-0.2878	0.5751	-0.0465	0.145	0.1228	-0.0847	0.0146	-0.0086	-0.0208	0.0064	0.0319	0.0338	-0.0152	0.0024	0.0357	0.013	0.0334	-7.487	30.522	-16.413
10	6.3242	2.785	-1.0732	2.3753	1.4792	3.8856	0.2211	0.2075	0.4777	0.2815	0.0649	0.3246	-0.2117	0.0388	-0.286	0.4534	0.0502	0.3461	0.2258	-0.0355	0.3363	6.513	-29.913	-13.402
11	2.4784	1.8761	0.1522	2.4693	1.1868	1.1099	0.1823	-0.249	0.0182	0.448	-0.2931	0.1232	0.301	-0.0914	0.1107	0.1474	-0.0667	0.0086	0.1708	0.0805	0.0752	3.61	-39.738	-16.974
12	3.0927	-0.7106	3.1294	7.1033	2.1238	4.4026	0.0758	-0.0669	-0.0088	0.0861	-0.0227	-0.2149	-0.0021	-0.1368	-0.0531	0.1075	0.0328	0.0145	0.0312	-0.0127	0.0726	10.591	-30.826	-22.031
13	4.7534	2.6799	-1.0251	43.1659	-1.5768	0.3663	0.01	0.2545	0.324	-0.5108	0.0715	0.3284	-0.1798	-0.0413	-0.0816	0.2962	-0.0117	-0.01	0.0596	0.0341	0.0451	13.706	-25.876	-24.396
14	5.7701	-3.4259	0.2958	9.2732	2.4894	4.0771	-0.3366	-0.4199	-0.1043	0.4065	0.6268	-0.346	0.5369	0.1869	-0.2901	0.1009	0.0414	-0.0349	0.0664	0.011	0.0835	14.499	-43.461	-22.908
15	1.9029	-3.9268	-3.1361	8.8692	3.3552	17.8514	0.0016	-0.2675	0.0634	0.117	0.5058	-0.0395	-0.502	0.651	-0.5075	0.06	-0.0838	0.0089	0.1937	-0.0532	0.2259	22.59	-31.485	-19.433
16	14.1725	7.8134	-4.9011	9.8727	-5.2812	3.2035	0.0895	-0.8919	-0.4441	-0.1026	-0.3405	-0.0275	0.0912	0.1369	0.2509	0.0682	-0.0436	0.0232	0.1163	-0.0222	0.141	10.443	-41.742	-15.627
17	14.3813	14.2291	2.6766	15.274	2.4885	9.6062	0.2699	-0.1503	-0.2373	0.0749	-0.0382	-0.1305	0.0169	0.1161	-0.2317	0.072	0.0074	0.0125	0.0565	0.0061	0.081	13.072	-35.666	-12.713
18	1.5568	0.0256	3.025	7.3839	4.4276	8.6422	-0.1638	-0.004	0.1634	0.3558	0.0409	-0.2159	-0.3727	-0.0758	0.1229	0.2763	0.0647	0.0889	0.0428	0.0395	0.0882	13.089	-26.052	-17.568
19	0.0926	-0.5739	0.0316	5.5893	-3.132	7.7824	0.0538	0.0674	-0.0353	-0.2917	0.0356	0.7557	-0.0372	-0.31	-0.0894	0.0529	0.0044	-0.0251	0.1788	0.1439	0.2958	11.215	-37.977	-31.415
20	4.7875	1.0442	3.4404	5.3649	3.9152	8.2896	-0.1145	-0.2362	0.4509	-0.0113	-0.1278	0.5309	-0.6188	-0.3931	0.2423	0.122	0.0311	0.0476	0.0944	0.0375	0.1458	6.796	-27.388	-19.281
21	2.9289	-0.0559	1.6466	2.4203	0.4153	3.7162	-0.0102	-0.0302	0.2712	-0.0178	-0.0518	0.1782	-0.0508	-0.4033	0.062	0.1508	-0.0206	0.0698	0.1006	-0.0141	0.0809	-6.707	10.605	-34.124
22	0.7053	1.179	0.7294	2.8365	1.0401	0.8296	0.089	-0.2132	0.2832	-0.0397	-0.3836	0.4289	0.1985	-0.1856	0.2945	0.2387	-0.0509	0.0933	0.1376	-0.0976	0.2854	0.894	11.673	-34.718
23	2.1798	-1.1009	1.6714	1.8737	-1.2168	2.5877	0.048	0.2502	-0.1334	-0.1865	0.0173	-0.1258	0.1003	0.1884	-0.0653	0.0287	-0.0174	0.0187	0.0698	-0.0079	0.0755	30.9	38.245	-33.59
24	0.9099	1.0571	0.169	1.6744	0.0777	0.2007	0.0619	0.0498	-0.2	0.0958	-0.0398	-0.3302	0.1006	0.0633	-0.0221	0.1216	0.0085	0.0049	0.0314	0.0018	0.141	22.424	18.663	-27.303
25	3.1527	1.8372	1.6172	3.7933	0.4203	1.0426	0.09	-0.0826	-0.1816	0.1732	-0.0716	-0.4143	0.0803	0.0187	-0.0184	0.2025	0.0005	0.0161	0.037	-0.0021	0.1129	18.195	-3.178	-24.88
26	0.9726	1.0888	-0.252	4.5836	-2.2427	1.2174	0.0109	0.0529	-0.1282	-0.279	0.0384	0.0012	0.1966	-0.0292	-0.0494	0.2045	-0.0145	0.0232	0.0829	-0.0219	0.0329	-0.932	6.303	-50.109
27	1.5081	-0.1998	0.6567	1.4955	-0.3658	0.8645	-0.0785	0.163	0.2282	-0.0354	-0.033	-0.0536	-0.0694	0.0892	0.1114	0.0498	-0.0003	0.0001	0.0733	0.0155	0.0523	4.956	47.519	-60.244

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	1 - 15
2	X-RAY DIFFRACTION	2	B	16 - 39
3	X-RAY DIFFRACTION	3	B	40 - 51
4	X-RAY DIFFRACTION	4	B	52 - 67
5	X-RAY DIFFRACTION	5	B	68 - 125
6	X-RAY DIFFRACTION	6	A	200 - 394
7	X-RAY DIFFRACTION	7	A	395 - 498
8	X-RAY DIFFRACTION	8	A	499 - 734
9	X-RAY DIFFRACTION	9	A	735 - 922
10	X-RAY DIFFRACTION	10	D	1 - 16
11	X-RAY DIFFRACTION	11	D	17 - 32
12	X-RAY DIFFRACTION	12	D	33 - 39
13	X-RAY DIFFRACTION	13	D	40 - 51
14	X-RAY DIFFRACTION	14	D	52 - 60
15	X-RAY DIFFRACTION	15	D	61 - 67
16	X-RAY DIFFRACTION	16	D	68 - 77
17	X-RAY DIFFRACTION	17	D	78 - 84
18	X-RAY DIFFRACTION	18	D	85 - 99
19	X-RAY DIFFRACTION	19	D	100 - 110
20	X-RAY DIFFRACTION	20	D	111 - 125
21	X-RAY DIFFRACTION	21	C	293 - 358
22	X-RAY DIFFRACTION	22	C	359 - 394
23	X-RAY DIFFRACTION	23	C	395 - 471
24	X-RAY DIFFRACTION	24	C	472 - 529
25	X-RAY DIFFRACTION	25	C	530 - 623
26	X-RAY DIFFRACTION	26	C	624 - 734
27	X-RAY DIFFRACTION	27	C	735 - 921

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi