PDB-4us7: Sulfur SAD Phased Structure of a Type IV Pilus Protein from Shewa...

ID or keywords:

Entry

Database: PDB / ID: 4us7

Title

Sulfur SAD Phased Structure of a Type IV Pilus Protein from Shewanella oneidensis

Components

PILD PROCESSED PROTEIN

Keywords

CELL ADHESION / TYPE IV PILIN / SULFUR SAD / STRUCTURAL PROTEIN

Function / homology

Function and homology information

type IV pilus / type IV pilus assembly / type IV pilus-dependent motility / membrane
Similarity search - Function

Biological species

SHEWANELLA ONEIDENSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.96 Å

Authors

Gorgel, M. / Boeggild, A. / Ulstrup, J.J. / Mueller, U. / Weiss, M. / Nissen, P. / Boesen, T.

Citation

Journal: Bmc Struct.Biol. / Year: 2015
Title: High-Resolution Structure of a Type Iv Pilin from the Metal- Reducing Bacterium Shewanella Oneidensis.
Authors: Gorgel, M. / Ulstrup, J.J. / Boggild, A. / Jones, N.C. / Hoffmann, S.V. / Nissen, P. / Boesen, T.

History

Deposition	Jul 3, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 29, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4us7.cif.gz	82.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4us7.ent.gz	67.9 KB	Display	PDB format
PDBx/mmJSON format	4us7.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/us/4us7 ftp://data.pdbj.org/pub/pdb/validation_reports/us/4us7	HTTPS FTP

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Related structure data

Related structure data	4d40C C: citing same article (ref.)
Similar structure data	4d40-1 4d40-2 5mix-d 6msv-8 4mal-2 1dxn-d 1puy-d 6du9-d 2920 4ab0-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
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (3)

Deposited unit

A: PILD PROCESSED PROTEIN

B: PILD PROCESSED PROTEIN

hetero molecules

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

1

A: PILD PROCESSED PROTEIN

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

2

B: PILD PROCESSED PROTEIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.830, 96.550, 109.760
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	PILD PROCESSED PROTEIN / TYPE IV PILUS PROTEIN Mass: 9913.945 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 36-123 Source method: isolated from a genetically manipulated source Details: CYSTEINE BRIDGE BETWEEN CYS69 AND CYS86 IN CHAIN A CYSTEINE BRIDGE BETWEEN CYS69 AND CYS86 IN CHAIN B Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Strain: MR-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ORIGAMI / References: UniProt: Q8EII5
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	N-TERMINAL G REMAINDER OF TEV CLEAVAGE SITE

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.27 Å³/Da / Density % sol: 62.4 % / Description: DATA WERE COLLECTED FOR SULFUR SAD
Crystal grow	pH: 8 / Details: 28% PEG 8K 100 MM TAPS PH 8.0 150 MM AMS

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.8
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2014 / Details: MIRRORS
Radiation	Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.8 Å / Relative weight: 1
Reflection	Resolution: 1.96→48.8 Å / Num. obs: 34976 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 17.5 % / B_iso Wilson estimate: 27.36 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 51.72
Reflection shell	Resolution: 1.96→2.01 Å / Redundancy: 13.9 % / R_merge(I) obs: 0.08 / Mean I/σ(I) obs: 21.15 / % possible all: 94.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.96→48.275 Å / SU ML: 0.18 / σ(F): 1.46 / Phase error: 21.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2201	3473	9.9 %
R_work	0.1794	-	-
obs	0.1835	34971	97.11 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 34.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→48.275 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1400	0	6	125	1531

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1450
X-RAY DIFFRACTION	f_angle_d	1.021	1969
X-RAY DIFFRACTION	f_dihedral_angle_d	11.822	525
X-RAY DIFFRACTION	f_chiral_restr	0.045	201
X-RAY DIFFRACTION	f_plane_restr	0.005	261

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9599-1.9868	0.2322	137	0.1667	1220	X-RAY DIFFRACTION	95
1.9868-2.0152	0.2032	135	0.1696	1244	X-RAY DIFFRACTION	95
2.0152-2.0453	0.1878	136	0.1669	1208	X-RAY DIFFRACTION	95
2.0453-2.0772	0.2436	133	0.1775	1241	X-RAY DIFFRACTION	95
2.0772-2.1113	0.2271	138	0.185	1206	X-RAY DIFFRACTION	93
2.1113-2.1477	0.2208	139	0.1875	1257	X-RAY DIFFRACTION	96
2.1477-2.1867	0.2698	137	0.1814	1213	X-RAY DIFFRACTION	95
2.1867-2.2288	0.1941	136	0.1793	1228	X-RAY DIFFRACTION	95
2.2288-2.2743	0.2444	132	0.1843	1233	X-RAY DIFFRACTION	96
2.2743-2.3237	0.2968	136	0.1913	1244	X-RAY DIFFRACTION	95
2.3237-2.3778	0.223	138	0.1925	1275	X-RAY DIFFRACTION	98
2.3778-2.4373	0.245	139	0.1848	1238	X-RAY DIFFRACTION	95
2.4373-2.5032	0.2758	134	0.2061	1271	X-RAY DIFFRACTION	98
2.5032-2.5768	0.2574	143	0.2026	1274	X-RAY DIFFRACTION	96
2.5768-2.66	0.2525	144	0.2018	1290	X-RAY DIFFRACTION	99
2.66-2.755	0.2279	138	0.1905	1261	X-RAY DIFFRACTION	97
2.755-2.8653	0.2815	141	0.2085	1277	X-RAY DIFFRACTION	98
2.8653-2.9957	0.2264	141	0.1928	1264	X-RAY DIFFRACTION	99
2.9957-3.1536	0.23	143	0.2008	1277	X-RAY DIFFRACTION	99
3.1536-3.3512	0.2203	139	0.1913	1300	X-RAY DIFFRACTION	99
3.3512-3.6098	0.1993	139	0.1787	1274	X-RAY DIFFRACTION	99
3.6098-3.973	0.2124	143	0.1641	1311	X-RAY DIFFRACTION	100
3.973-4.5475	0.1937	142	0.1543	1297	X-RAY DIFFRACTION	100
4.5475-5.7279	0.1769	146	0.1529	1290	X-RAY DIFFRACTION	100
5.7279-48.2896	0.1966	144	0.1698	1305	X-RAY DIFFRACTION	100

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	5.3556	-2.1442	-4.0427	7.4398	4.7399	9.1793	0.1823	0.0103	0.0069	0.1259	-0.1255	0.1132	-0.1598	-0.6446	0.0793	0.1494	-0.0108	-0.0207	0.2542	0.0113	0.1965	10.4949	42.0112	35.8884
2	1.6308	-0.2498	-1.1971	4.6866	1.3972	4.2939	0.0317	0.1612	0.0404	-0.1089	0.0844	-0.3743	-0.1966	-0.151	-0.1192	0.1423	0.0201	-0.0173	0.1658	-0.0287	0.2591	18.4284	45.9079	33.0302
3	4.2822	-0.6044	-0.8677	2.3834	0.8182	7.3489	-0.0504	-0.1945	0.5884	0.9358	0.21	-0.2355	-0.228	-0.3204	-0.157	0.4193	0.0569	-0.0679	0.2207	-0.0585	0.3466	14.8152	51.1964	45.8593
4	6.3985	-0.5544	-4.0692	5.2893	2.2387	3.3573	-0.4887	-0.3231	0.3411	1.236	0.3145	-0.2538	0.975	-0.0917	0.2006	0.4483	0.026	-0.0735	0.2303	-0.0156	0.2903	15.452	39.0722	45.5571
5	6.5285	-1.1259	-2.6172	5.9815	2.6048	8.9415	0.2105	0.4814	0.0812	-0.339	-0.082	0.0196	-0.3326	-0.1592	-0.1219	0.1525	0.0297	-0.0453	0.1694	-0.0078	0.2265	1.843	31.9153	30.1028
6	3.0278	-0.3675	-0.5963	3.2271	0.318	7.0109	0.1428	0.412	-0.5485	-0.1344	0.0523	-0.1139	0.4439	0.1226	-0.2318	0.1651	0.0106	-0.0538	0.2403	-0.1019	0.2823	7.8512	24.7311	29.5191
7	5.9405	-0.4962	1.4527	4.8084	0.7542	7.6524	0.0444	-0.5181	-0.266	0.5254	-0.1605	0.2219	-0.0396	-0.3405	0.0622	0.2266	-0.0368	0.0127	0.1998	0.0054	0.2805	-2.1614	25.3721	38.3835

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 27 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 28 THROUGH 61 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 62 THROUGH 75 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 76 THROUGH 89 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 1 THROUGH 27 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 28 THROUGH 61 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 62 THROUGH 89 )

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