PDB-8deo: Structure of AAP A domain and B-repeats (residues 351-813) from S...

ID or keywords:

Entry

Database: PDB / ID: 8deo

Title

Structure of AAP A domain and B-repeats (residues 351-813) from Staphylococcus epidermidis

Components

Accumulation associated protein

Keywords

CELL ADHESION / L-type lectin / Staphylococcus epidermidis

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Staphylococcus epidermidis RP62A (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Harris, G. / Whelan, F. / Clark, L. / Turkenburg, J.P. / Potts, J.R.

Funding support

United Kingdom, 3items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/J005029/	United Kingdom
British Heart Foundation	FS/12/36/29588	United Kingdom
British Heart Foundation	PG/17/19/32862	United Kingdom

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Staphylococcal Periscope proteins Aap, SasG, and Pls project noncanonical legume-like lectin adhesin domains from the bacterial surface.
Authors: Clark, L.C. / Atkin, K.E. / Whelan, F. / Brentnall, A.S. / Harris, G. / Towell, A.M. / Turkenburg, J.P. / Liu, Y. / Feizi, T. / Griffiths, S.C. / Geoghegan, J.A. / Potts, J.R.

History

Deposition	Jun 21, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8deo.cif.gz	454.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8deo.ent.gz	284.6 KB	Display	PDB format
PDBx/mmJSON format	8deo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8deo_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	8deo_full_validation.pdf.gz	1.3 MB	Display
Data in XML	8deo_validation.xml.gz	32.5 KB	Display
Data in CIF	8deo_validation.cif.gz	46 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/de/8deo ftp://data.pdbj.org/pub/pdb/validation_reports/de/8deo	HTTPS FTP

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Related structure data

Related structure data	7sieSC 7sjkC 7smhC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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: Accumulation associated protein

B: Accumulation associated protein

hetero molecules

101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Accumulation associated protein

hetero molecules

defined by author
Evidence: SAXS, Predicted scattering by monomeric Aap 351-813 fits the measured solution scattering with a Chi-squared value of 1.1
50.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Accumulation associated protein

hetero molecules

defined by author
50.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.482, 66.565, 66.873
Angle α, β, γ (deg.)	84.695, 80.489, 89.664
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 352 - 813 / Label seq-ID: 6 - 467

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Accumulation associated protein Mass: 50670.117 Da / Num. of mol.: 2 / Fragment: residues 351-813 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis RP62A (bacteria) Strain: ATCC 35984 / RP62A / Gene: aap, SERP2398 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HKE8
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.54 Å³/Da / Density % sol: 51.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 550 MME, 10% PEG 20K, 100 mM MOPS/HEPES pH 7 (Morpheus Buffer System 2)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.3→39.709 Å / Num. obs: 42896 / % possible obs: 97.5 % / Redundancy: 2.2 % / CC_1/2: 0.989 / R_merge(I) obs: 0.08 / R_pim(I) all: 0.08 / R_rim(I) all: 0.113 / Net I/σ(I): 4.8
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.586 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4169 / CC_1/2: 0.764 / R_pim(I) all: 0.586 / R_rim(I) all: 0.829 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
xia2		data reduction
Aimless	0.7.7	data scaling
MOLREP	11.7.03	phasing
Coot	0.9.8.1	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7SIE

7sie

Resolution: 2.3→39.709 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.929 / WR_factor R_free: 0.254 / WR_factor R_work: 0.204 / SU B: 19.63 / SU ML: 0.226 / Average fsc free: 0.9524 / Average fsc work: 0.9615 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.235
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2426	2120	4.942 %	RANDOM
R_work	0.1975	40775	-	-
all	0.2	-	-	-
obs	-	42895	97.517 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 51.537 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.365 Å²	0.378 Å²	0.289 Å²
2-	-	-2.534 Å²	-1.177 Å²
3-	-	-	5.386 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→39.709 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6692	0	4	168	6864

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.011	6871
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5790
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.056	0.1	47566
X-RAY DIFFRACTION	r_angle_refined_deg	1.407	1.672	9355
X-RAY DIFFRACTION	r_angle_other_deg	0.492	1.565	13604
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.534	5	908
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.264	10	23
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.058	10	991
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.408	10	304
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	1016
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8029
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1263
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	1033
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	5086
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	3279
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	3648
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	221
X-RAY DIFFRACTION	r_metal_ion_refined	0.2	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.125	0.2	37
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	157
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.132	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	2.266	2.919	3637
X-RAY DIFFRACTION	r_mcbond_other	2.266	2.92	3636
X-RAY DIFFRACTION	r_mcangle_it	3.589	4.373	4539
X-RAY DIFFRACTION	r_mcangle_other	3.589	4.373	4540
X-RAY DIFFRACTION	r_scbond_it	2.384	2.966	3234
X-RAY DIFFRACTION	r_scbond_other	2.384	2.966	3235
X-RAY DIFFRACTION	r_scangle_it	3.649	4.404	4815
X-RAY DIFFRACTION	r_scangle_other	3.649	4.403	4816
X-RAY DIFFRACTION	r_lrange_it	6.829	99.235	51677
X-RAY DIFFRACTION	r_lrange_other	6.829	99.248	51663
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.066	0.05	13062

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06635	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06635	0.05009

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	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.3-2.36	0.313	154	0.326	2988	0.325	3248	0.896	0.902	96.7365	0.324
2.36-2.424	0.3	146	0.294	2890	0.294	3123	0.934	0.93	97.2142	0.289
2.424-2.494	0.285	152	0.276	2839	0.276	3068	0.944	0.938	97.4902	0.27
2.494-2.57	0.311	127	0.27	2814	0.272	3022	0.926	0.946	97.3197	0.268
2.57-2.654	0.278	147	0.239	2678	0.241	2907	0.954	0.96	97.1792	0.232
2.654-2.747	0.254	125	0.224	2580	0.226	2769	0.961	0.961	97.6887	0.217
2.747-2.85	0.261	125	0.229	2508	0.231	2709	0.952	0.965	97.1945	0.22
2.85-2.966	0.267	151	0.21	2382	0.213	2599	0.956	0.971	97.4606	0.202
2.966-3.097	0.253	131	0.204	2331	0.206	2521	0.955	0.975	97.6597	0.198
3.097-3.247	0.248	97	0.194	2229	0.196	2378	0.96	0.977	97.8133	0.19
3.247-3.422	0.245	117	0.201	2120	0.203	2282	0.961	0.978	98.028	0.197
3.422-3.628	0.255	100	0.2	1993	0.203	2141	0.963	0.977	97.7581	0.202
3.628-3.876	0.253	100	0.181	1902	0.185	2042	0.963	0.981	98.0411	0.184
3.876-4.183	0.197	101	0.152	1755	0.155	1884	0.978	0.983	98.5138	0.159
4.183-4.577	0.188	83	0.138	1581	0.14	1699	0.982	0.989	97.94	0.154
4.577-5.109	0.172	83	0.14	1464	0.142	1582	0.986	0.988	97.7876	0.161
5.109-5.883	0.255	54	0.176	1298	0.179	1377	0.967	0.982	98.1845	0.203
5.883-7.166	0.3	47	0.195	1098	0.198	1177	0.954	0.977	97.2812	0.221
7.166-9.973	0.216	61	0.182	831	0.184	921	0.972	0.979	96.8512	0.211
9.973-39.709	0.252	19	0.188	493	0.19	528	0.962	0.977	96.9697	0.227

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	2.3411	0.1212	-0.1067	3.0757	0.2266	1.7589	0.1243	0.0694	-0.154	0.0228	-0.086	0.0247	0.1495	-0.0188	-0.0383	0.1388	0.0044	-0.0735	0.005	-0.0089	0.0673	-35.6775	13.1951	5.988
2	8.6018	-2.936	1.7565	1.3148	-0.674	0.3765	0.0661	0.5648	0.1923	-0.0657	-0.1401	-0.1982	0.0177	0.0982	0.074	0.5964	0.122	0.0184	0.8258	-0.0837	0.8474	17.1122	-8.5072	-9.4604
3	3.8307	-3.3515	1.165	4.9531	-1.065	2.2017	0.0321	0.0404	0.2307	0.123	-0.0647	1.0318	-0.297	-0.9301	0.0325	0.2828	0.1319	0.0096	0.4846	-0.0027	0.7999	66.9067	-23.9877	-10.4412
4	6.5902	-3.3377	-1.1627	1.7102	0.595	0.2079	0.0412	0.0552	0.5402	-0.0294	0.0656	-0.2684	-0.0026	0.0231	-0.1068	0.379	0.0661	0.0531	0.4634	-0.0068	0.4186	115.7852	-44.949	-12.9768
5	2.0909	0.0528	-0.0647	3.2448	-0.2352	1.7647	0.0765	-0.0488	-0.1288	-0.0411	-0.0778	0.0847	0.1498	0.0685	0.0013	0.1125	-0.0239	-0.0438	0.0298	-0.014	0.0682	24.4168	46.5706	21.8197
6	8.0951	1.5712	-0.3438	2.6683	-0.0081	1.6809	0.0212	0.0072	-0.3312	-0.0786	-0.057	0.3583	0.1254	-0.1796	0.0358	0.4211	0.0013	-0.0129	0.4087	0.078	0.4592	-38.5523	20.1346	36.6455
7	6.6084	2.3751	0.1626	0.9236	0.0585	0.0324	0.2864	-0.4167	0.5973	0.1111	-0.2584	0.0293	0.0024	0.1012	-0.028	0.3287	-0.1137	-0.0169	0.639	0.0924	0.605	-53.1565	17.7811	37.458
8	9.2405	4.6745	-0.9568	2.3755	-0.4774	0.1108	0.3007	-0.3963	-0.0207	0.2068	-0.2253	-0.0483	-0.0304	0.0118	-0.0754	0.3744	-0.0932	0.0196	0.4926	0.0656	0.437	-128.6744	-12.8261	40.6342

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	351 - 612
2	X-RAY DIFFRACTION	2	ALL	A	613 - 685
3	X-RAY DIFFRACTION	3	ALL	A	686 - 737
4	X-RAY DIFFRACTION	4	ALL	A	738 - 813

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