PDB-5n8p: S-layer protein RsaA from C. crescentus

基本情報

• 登録情報: データベース: PDB / ID: 5n8p
• タイトル: S-layer protein RsaA from C. crescentus
• 要素: S-layer protein
• キーワード: MEMBRANE PROTEIN / S-layer / surface protein
• 機能・相同性: RsaA N-terminal domain / S-layer / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / calcium ion binding / extracellular region / S-layer protein
• 生物種: Caulobacter crescentus CB15 (バクテリア)
• 手法: X線回折 / シンクロトロン / 解像度: 2.7 Å
• データ登録者: Bharat, T.A.M. / Kureisaite-Ciziene, D. / Lowe, J.
• 引用: ジャーナル: Nat Microbiol / 年: 2017; タイトル: Structure of the hexagonal surface layer on Caulobacter crescentus cells.; 著者: Tanmay A M Bharat / Danguole Kureisaite-Ciziene / Gail G Hardy / Ellen W Yu / Jessica M Devant / Wim J H Hagen / Yves V Brun / John A G Briggs / Jan Löwe / ; 要旨: Many prokaryotic cells are encapsulated by a surface layer (S-layer) consisting of repeating units of S-layer proteins. S-layer proteins are a diverse class of molecules found in Gram-positive and Gram-negative bacteria and most archaea. S-layers protect cells from the outside, provide mechanical stability and also play roles in pathogenicity. In situ structural information about this highly abundant class of proteins is scarce, so atomic details of how S-layers are arranged on the surface of cells have remained elusive. Here, using purified Caulobacter crescentus' sole S-layer protein RsaA, we obtained a 2.7 Å X-ray structure that shows the hexameric S-layer lattice. We also solved a 7.4 Å structure of the S-layer through electron cryotomography and sub-tomogram averaging of cell stalks. The X-ray structure was docked unambiguously into the electron cryotomography map, resulting in a pseudo-atomic-level description of the in vivo S-layer, which agrees completely with the atomic X-ray lattice model. The cellular S-layer atomic structure shows that the S-layer is porous, with a largest gap dimension of 27 Å, and is stabilized by multiple Ca ions bound near the interfaces. This study spans different spatial scales from atoms to cells by combining X-ray crystallography with electron cryotomography and sub-nanometre-resolution sub-tomogram averaging.

履歴

登録	2017年2月24日	登録サイト: PDBE / 処理サイト: PDBE
改定 1.0	2017年4月12日	Provider: repository / タイプ: Initial release
改定 1.1	2017年4月26日	Group: Database references
改定 1.2	2019年2月20日	Group: Advisory / Data collection / Derived calculations カテゴリ: diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type Item: _diffrn_source.pdbx_synchrotron_site
改定 1.3	2019年7月10日	Group: Data collection / カテゴリ: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
改定 1.4	2024年5月8日	Group: Data collection / Database references / Derived calculations / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

集合体

登録構造単位

A: S-layer protein

B: S-layer protein

C: S-layer protein

D: S-layer protein

E: S-layer protein

F: S-layer protein

ヘテロ分子

概要:

• 593 kDa, 6 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	593,492	120
ポリマ－	588,923	6
非ポリマー	4,569	114
水	2,648	147

1

概要:

• 登録構造と同一
• 登録者・ソフトウェアが定義した集合体
• 根拠: microscopy, RsaA polymerises to form a 2D lattice on cells and also in the crystals. This was determined by comparing the crystal packing described here with electron tomography data from cells (submitted in separate EMDB entry, to be submitted).

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555	x,y,z	1

計算値:

Buried area	10150 Å2
ΔGint	-714 kcal/mol
Surface area	168930 Å2
手法	PISA

単位格子

Length a, b, c (Å)	215.880, 74.960, 221.660
Angle α, β, γ (deg.)	90.00, 118.99, 90.00
Int Tables number	4
Space group name H-M	P1211

非結晶学的対称性 (NCS)

NCSドメイン:

ID	Ens-ID	詳細
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	B
2	6	C
1	7	B
2	7	D
1	8	B
2	8	E
1	9	B
2	9	F
1	10	C
2	10	D
1	11	C
2	11	E
1	12	C
2	12	F
1	13	D
2	13	E
1	14	D
2	14	F
1	15	E
2	15	F

NCSドメイン領域:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 249 - 1026 / Label seq-ID: 249 - 1026

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	B	B
2	6	C	C
1	7	B	B
2	7	D	D
1	8	B	B
2	8	E	E
1	9	B	B
2	9	F	F
1	10	C	C
2	10	D	D
1	11	C	C
2	11	E	E
1	12	C	C
2	12	F	F
1	13	D	D
2	13	E	E
1	14	D	D
2	14	F	F
1	15	E	E
2	15	F	F

NCSアンサンブル:

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

要素

#1: タンパク質

A B C D E F
S-layer protein / Paracrystalline surface layer protein

詳細:

分子量: 98153.906 Da / 分子数: 6 / 由来タイプ: 天然
由来: (天然) Caulobacter crescentus CB15 (バクテリア)
参照: UniProt: P35828

#2: 化合物

A-9001 A-9002 A-9003 A-9004 A-9005 A-9006 A-9007 A-9008 A-9009 A-9010 A-9011 A-9012 A-9013 A-9014 A-9015 A-9016 A-9017 A-9018 A-9019 B-9001 ...
ChemComp-CA / CALCIUM ION / カルシウムジカチオン

詳細:

分子量: 40.078 Da / 分子数: 114 / 由来タイプ: 合成 / 式: Ca

#3: 水

ChemComp-HOH / water

詳細:

分子量: 18.015 Da / 分子数: 147 / 由来タイプ: 天然 / 式: H₂O

実験情報

実験

• 実験: 手法: X線回折 / 使用した結晶の数: 1

試料調製

• 結晶: マシュー密度: 2.66 ų/Da / 溶媒含有率: 53.83 %
• 結晶化: 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 ; 詳細: 0.07 M KSCN, 24 % 318 (w/v) PEG 8000, 0.075 M TAPS pH 8.5

データ収集

• 回折: 平均測定温度: 100 K
• 放射光源: 由来: シンクロトロン / サイト: Diamond / ビームライン: I04 / 波長: 0.97948 Å
• 検出器: タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年6月29日
• 放射: プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
• 放射波長: 波長: 0.97948 Å / 相対比: 1
• 反射: 解像度: 2.7→50 Å / Num. obs: 160466 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.1 % / CC_1/2: 0.99 / R_merge(I) obs: 0.181 / R_pim(I) all: 0.122 / Net I/σ(I): 5.5
• 反射 シェル: 解像度: 2.7→2.85 Å / 冗長度: 3.1 % / R_merge(I) obs: 1.315 / Mean I/σ(I) obs: 1 / Num. unique obs: 23593 / CC_1/2: 0.565 / R_pim(I) all: 0.89 / % possible all: 98.3

解析

ソフトウェア

名称	バージョン	分類
REFMAC	5.8.0155	精密化
XDS		データ削減
SCALA		データスケーリング
PHASER		位相決定

精密化

解像度: 2.7→50 Å / Cor.coef. F_o:F_c: 0.858 / Cor.coef. F_o:F_c free: 0.84 / SU B: 15.886 / SU ML: 0.309 / 交差検証法: THROUGHOUT / ESU R Free: 0.448

	Rfactor	反射数	%反射	Selection details
Rfree	0.27583	6102	5.1 %	RANDOM
Rwork	0.25799	-	-	-
obs	0.2589	113291	69.63 %	-

• 溶媒の処理: イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å

原子変位パラメータ

B_iso mean: 23.071 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.88 Å2	0 Å2	0.41 Å2
2-	-	-2.72 Å2	0 Å2
3-	-	-	0.86 Å2

精密化ステップ

サイクル: 1 / 解像度: 2.7→50 Å

	タンパク質	核酸	リガンド	溶媒	全体
原子数	30798	0	114	147	31059

拘束条件

Refine-ID	タイプ	Dev ideal	Dev ideal target	数
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.02	30995
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.859	1.932	42669
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.018	5	4661
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.722	27.164	804
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.439	15	3954
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.493	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	5946
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	22526
X-RAY DIFFRACTION	r_gen_planes_other
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	1.749	2.312	18665
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.968	3.467	23319
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.755	2.293	12330
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	7.333	32.67	42720
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

Refine-ID: X-RAY DIFFRACTION / タイプ: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	数
1	1	A	43760
1	2	B	43760
2	1	A	43734
2	2	C	43734
3	1	A	43710
3	2	D	43710
4	1	A	43770
4	2	E	43770
5	1	A	43726
5	2	F	43726
6	1	B	43762
6	2	C	43762
7	1	B	43800
7	2	D	43800
8	1	B	43736
8	2	E	43736
9	1	B	43842
9	2	F	43842
10	1	C	43768
10	2	D	43768
11	1	C	43728
11	2	E	43728
12	1	C	43728
12	2	F	43728
13	1	D	43706
13	2	E	43706
14	1	D	43798
14	2	F	43798
15	1	E	43738
15	2	F	43738

LS精密化 シェル

解像度: 2.7→2.77 Å / Total num. of bins used: 20

	Rfactor	反射数	%反射
Rfree	0.558	90	-
Rwork	0.508	1820	-
obs	-	-	15.11 %