PDB-9fsa: Cell wall anchoring domain of the surface layer protein of Methan...

ID or keywords:

Entry

Database: PDB / ID: 9fsa

Title

Cell wall anchoring domain of the surface layer protein of Methanococcus voltae (aa 24-75; 484-576)

Components

S-layer protein

Keywords

STRUCTURAL PROTEIN / Surface layer protein / self assembly / cell wall binding / anchoring / symmetry

Function / homology

S-layer protein / S-layer protein, N-terminal / S-layer protein, C-terminal / S-layer like family, central region / S-layer like family, outer domain / S-layer / cell wall organization / extracellular region / S-layer protein

Function and homology information

Biological species

Methanococcus voltae (archaea)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Grininger, C. / Sagmeister, T. / Pavkov-Keller, T.

Funding support

Austria, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: SymProFold: Structural prediction of symmetrical biological assemblies.
Authors: Buhlheller, C. / Sagmeister, T. / Grininger, C. / Gubensak, N. / Sleytr, U.B. / Uson, I. / Pavkov-Keller, T.

History

Deposition	Jun 20, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fsa.cif.gz	59.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9fsa.ent.gz	41.3 KB	Display	PDB format
PDBx/mmJSON format	9fsa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fsa_validation.pdf.gz	426.2 KB	Display	wwPDB validaton report
Full document	9fsa_full_validation.pdf.gz	428.1 KB	Display
Data in XML	9fsa_validation.xml.gz	7.1 KB	Display
Data in CIF	9fsa_validation.cif.gz	8.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fs/9fsa ftp://data.pdbj.org/pub/pdb/validation_reports/fs/9fsa	HTTPS FTP

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Related structure data

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: S-layer protein

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

1

A: S-layer protein

defined by author
Evidence: gel filtration
31.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.340, 53.268, 55.627
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	S-layer protein / Cell surface glycoprotein / Surface layer protein Mass: 15757.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus voltae (archaea) / Gene: sla Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q50833
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: JCSG+ eco condition C2 1.0 M LiCl, 0.1 M citrate pH 4.0, 20 % PEG 6000 0.3 ul condition + 0.3 ul protein solution

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3414 Å
Detector	Type: Bruker PHOTON III / Detector: PIXEL / Date: Jun 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3414 Å / Relative weight: 1
Reflection	Resolution: 2.05→46.34 Å / Num. obs: 4977 / % possible obs: 90.7 % / Redundancy: 23.5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.332 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.05→2.24 Å / Redundancy: 15.8 % / R_merge(I) obs: 1.8 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 291 / CC_1/2: 0.65 / % possible all: 70.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
PHENIX	1.20.1	refinement
DIALS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→46.34 Å / Cor.coef. F_o:F_c: 0.882 / Cor.coef. F_o:F_c free: 0.873 / SU B: 6.53 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.686 / ESU R Free: 0.324
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2825	286	5.75 %
R_work	0.2652	4688	-
all	0.266	-	-
obs	-	4974	54.725 %

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: 22.898 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.316 Å²	-0 Å²	0 Å²
2-	-	0.554 Å²	-0 Å²
3-	-	-	0.762 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→46.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	928	0	0	14	942

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	932
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	936
X-RAY DIFFRACTION	r_angle_refined_deg	1.075	1.609	1268
X-RAY DIFFRACTION	r_angle_other_deg	0.358	1.557	2164
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.047	5	133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.029	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.16	10	150
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.086	10	28
X-RAY DIFFRACTION	r_chiral_restr	0.044	0.2	167
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1058
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	142
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	190
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	974
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	491
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	603
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.205	0.2	19
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.31	0.2	56
X-RAY DIFFRACTION	r_mcbond_it	2.109	2.172	538
X-RAY DIFFRACTION	r_mcbond_other	2.107	2.172	538
X-RAY DIFFRACTION	r_mcangle_it	3.505	3.229	669
X-RAY DIFFRACTION	r_mcangle_other	3.504	3.235	670
X-RAY DIFFRACTION	r_scbond_it	2.054	2.589	394
X-RAY DIFFRACTION	r_scbond_other	2.052	2.594	395
X-RAY DIFFRACTION	r_scangle_it	3.552	3.717	599
X-RAY DIFFRACTION	r_scangle_other	3.549	3.722	600
X-RAY DIFFRACTION	r_lrange_it	8.812	41.803	4017
X-RAY DIFFRACTION	r_lrange_other	8.812	41.815	4017

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 work	% reflection obs (%)	WR_factor R_work	Fsc free
2.05-2.103		0	0.287	33	0.287	645	0.926	5.1163	0.277
2.103-2.161	0.322	3	0.355	87	0.354	639	0.893	14.0845	0.315	0.86
2.161-2.223	0.484	3	0.374	129	0.376	633	0.905	20.8531	0.36	0.809
2.223-2.291	0.36	5	0.272	147	0.275	593	0.949	25.6324	0.256	0.918
2.291-2.366	0.169	15	0.32	173	0.308	597	0.932	31.4908	0.302	0.96
2.366-2.449	0.419	13	0.302	206	0.308	573	0.935	38.2199	0.262	0.902
2.449-2.541	0.322	14	0.326	221	0.326	543	0.932	43.2781	0.312	0.956
2.541-2.645	0.297	16	0.343	236	0.34	533	0.932	47.2795	0.309	0.927
2.645-2.762	0.343	8	0.311	262	0.312	505	0.931	53.4653	0.267	0.85
2.762-2.896	0.382	19	0.329	293	0.333	496	0.928	62.9032	0.29	0.909
2.896-3.052	0.342	22	0.298	312	0.301	460	0.937	72.6087	0.266	0.957
3.052-3.237	0.348	24	0.288	355	0.291	454	0.941	83.4802	0.239	0.929
3.237-3.459	0.318	16	0.295	380	0.296	420	0.945	94.2857	0.254	0.925
3.459-3.734	0.277	23	0.249	359	0.251	393	0.959	97.201	0.21	0.951
3.734-4.088	0.192	14	0.236	347	0.234	362	0.963	99.7238	0.203	0.977
4.088-4.566	0.157	27	0.193	309	0.19	336	0.976	100	0.176	0.98
4.566-5.264	0.305	22	0.227	274	0.232	296	0.971	100	0.213	0.964
5.264-6.426	0.358	21	0.268	247	0.276	268	0.952	100	0.247	0.939
6.426-9.002	0.314	15	0.2	190	0.205	205	0.974	100	0.209	0.946
9.002-46.34	0.153	6	0.234	128	0.23	134	0.961	100	0.267	0.99

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