PDB-5ek5: STRUCTURAL CHARACTERIZATION OF IRMA FROM ESCHERICHIA COLI

ID or keywords:

Entry

Database: PDB / ID: 5ek5

Title

STRUCTURAL CHARACTERIZATION OF IRMA FROM ESCHERICHIA COLI

Components

IRMA

Keywords

UNKNOWN FUNCTION / FIBRONECTIN FOLD /

VIRULENCE /

SECRETED PROTEIN

Function / homology

Interleukin receptor mimic protein A / interleukin receptor mimic protein A /

FORMIC ACID / Uncharacterized protein / Uncharacterized protein

Function and homology information

Biological species

Escherichia coli CFT073 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.26 Å

Authors

Heras, B. / Moriel, D.G. / Paxman, J.J. / Schembri, M.A.

Citation

Journal: Mbio / Year: 2016
Title: Molecular and Structural Characterization of a Novel Escherichia coli Interleukin Receptor Mimic Protein.
Authors: Moriel, D.G. / Heras, B. / Paxman, J.J. / Lo, A.W. / Tan, L. / Sullivan, M.J. / Dando, S.J. / Beatson, S.A. / Ulett, G.C. / Schembri, M.A.

History

Deposition	Nov 3, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 30, 2016	Group: Database references
Revision 1.2	Jul 13, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ek5.cif.gz	109 KB	Display	PDBx/mmCIF format
PDB format	pdb5ek5.ent.gz	89 KB	Display	PDB format
PDBx/mmJSON format	5ek5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ek/5ek5 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/5ek5	HTTPS FTP

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Related structure data

Similar structure data	2ejq-d 3qwn-1 3gr1-5 3qwn-2 2y7s-2 4tmf-1 3a7g-1 3dzj-2 3k93-d 4rv0-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: IRMA

B: IRMA

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	93.999, 93.999, 93.999
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

Components on special symmetry positions

ID	Model	Components
1	1	A-201- CL
2	1	B-201- NA

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Protein , 1 types, 2 molecules AB

#1: Protein	IRMA Mass: 14369.842 Da / Num. of mol.: 2 / Fragment: UNP residues 25-151 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Strain: CFT073 Gene: ACM20_11530, HUS2011_3591, SK67_04736, SK69_02333, SK70_03200, SK71_02973, SK75_00406, SK76_00877, SK83_00395, SK84_04099, SK86_02365, SY51_17055 Plasmid: PMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q6KD75, UniProt: A0A0H2VAX3*PLUS

#1: Protein

IRMA

Mass: 14369.842 Da / Num. of mol.: 2 / Fragment: UNP residues 25-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli CFT073 (bacteria) / Strain: CFT073
Gene: ACM20_11530, HUS2011_3591, SK67_04736, SK69_02333, SK70_03200, SK71_02973, SK75_00406, SK76_00877, SK83_00395, SK84_04099, SK86_02365, SY51_17055
Plasmid: PMCSG7 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q6KD75, UniProt: A0A0H2VAX3*PLUS

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Non-polymers , 5 types, 120 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.37 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100 MM BIS-TRIS PROPANE PH 9.0 AND 2% (W/V) POLYETHYLENE GLYCOL (PEG) 2000, VAPOR DIFFUSION, TEMPERATURE 294K PH range: 9

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
ROTATING ANODE			RIGAKU FR-E SUPERBRIGHT	1	1.5418
SYNCHROTRON	Australian Synchrotron	MX2		2	0.9686

Detector

Type	ID	Detector	Date	Details
RIGAKU SATURN 944	1	CCD	Jul 17, 2012	MIRRORS
ADSC QUANTUM 210r	2	CCD	Aug 24, 2012	MIRRORS

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	0.9686	1

Reflection

Resolution: 2.26→47 Å / Num. obs: 13278 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.7 % / R_merge(I) obs: 0.063 / Net I/σ(I): 37.1

Reflection shell

Resolution: 2.26→2.34 Å / Redundancy: 21.2 % / R_merge(I) obs: 0.859 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	dev_1760	refinement
HKL-2000		data reduction
HKL-2000		data scaling
Auto-Rickshaw		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.26→47 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.261	1873	14.13 %	Random selection
R_work	0.215	-	-	-
obs	0.222	13251	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 53.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.26→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1864	0	9	116	1989

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1905
X-RAY DIFFRACTION	f_angle_d	1.09	2584
X-RAY DIFFRACTION	f_dihedral_angle_d	13.195	694
X-RAY DIFFRACTION	f_chiral_restr	0.043	298
X-RAY DIFFRACTION	f_plane_restr	0.004	339

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 (%)
2.26-2.3197	0.3643	156	0.3215	820	X-RAY DIFFRACTION	100
2.3197-2.388	0.3071	127	0.2773	896	X-RAY DIFFRACTION	100
2.388-2.465	0.3116	160	0.27	826	X-RAY DIFFRACTION	100
2.465-2.5531	0.3184	148	0.2626	874	X-RAY DIFFRACTION	100
2.5531-2.6554	0.2913	123	0.2507	878	X-RAY DIFFRACTION	100
2.6554-2.7762	0.3073	141	0.2761	873	X-RAY DIFFRACTION	100
2.7762-2.9225	0.3207	140	0.2553	871	X-RAY DIFFRACTION	100
2.9225-3.1056	0.3208	141	0.2426	874	X-RAY DIFFRACTION	100
3.1056-3.3453	0.2832	153	0.2313	868	X-RAY DIFFRACTION	100
3.3453-3.6819	0.2546	130	0.2059	889	X-RAY DIFFRACTION	100
3.6819-4.2144	0.218	151	0.1747	877	X-RAY DIFFRACTION	100
4.2144-5.3085	0.1924	124	0.1503	926	X-RAY DIFFRACTION	100
5.3085-47.0097	0.2438	179	0.2206	906	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	6.4322	3.01	0.7273	5.977	-1.1313	7.1938	-0.2075	-0.6912	0.238	0.5109	0.0994	0.0869	-0.2756	0.3807	0.1342	0.327	-0.0745	0.0087	0.2405	0.0073	0.1047	31.7722	-2.7508	9.9593
2	6.752	1.6251	-2.6618	3.603	-0.2007	2.4274	-0.2031	0.3326	0.0025	0.1156	0.0956	0.5133	0.3818	-0.4186	0.1439	0.336	-0.0588	0.0174	0.4153	0.0033	0.235	19.6229	-8.2818	5.7384
3	2.0282	-2.1228	2.0264	7.4875	0.2471	6.8554	0.1845	0.0857	0.3401	-0.1864	0.0144	0.047	0.4702	0.1105	-0.0196	0.303	-0.0879	0.0351	0.2218	0.0572	0.2087	35.961	-1.1493	6.7788
4	9.7188	-7.6369	-0.9885	5.9983	0.7778	0.1011	0.6074	1.3118	-0.4759	-1.2042	-0.7324	0.0888	-0.1346	-0.4608	0.1596	0.4686	-0.1139	-0.1085	0.7864	0.0956	0.6366	13.2599	-0.4973	9.1716
5	3.6596	-1.9773	-3.7658	2.1287	2.3746	6.4999	-0.1792	0.0543	-0.2927	0.1574	0.1143	-0.0415	0.7733	-0.2148	0.154	0.3864	-0.0659	-0.0087	0.2451	0.0318	0.2946	29.8973	-9.8466	10.1524
6	7.3049	1.2208	-2.5755	2.0997	-1.7595	6.9575	-0.2955	-0.1354	0.1879	0.0157	0.0311	0.0378	0.2499	0.9676	0.1931	0.4007	0.0291	-0.0196	0.5637	-0.0119	0.2217	29.5172	-1.5706	30.682
7	5.9829	-8.8614	-5.356	1.9899	7.9341	4.7915	1.4876	-1.6118	1.3741	-1.3437	-0.2933	-1.2375	-1.8946	0.693	-1.1609	0.3122	-0.2714	0.1414	1.2987	-0.3074	0.7756	43.8923	8.1658	27.3985
8	2.3281	0.345	-1.8947	3.8875	0.0657	4.1922	0.0225	-0.5668	0.3466	0.5233	-0.1669	0.1467	-0.9128	0.4699	0.1292	0.5145	-0.0371	-0.0286	0.4341	-0.085	0.2687	21.9381	5.6333	36.0015
9	3.7695	0.9171	-0.0046	8.1428	-0.9812	6.957	-0.1081	-0.6479	-0.3595	0.2716	0.0931	-1.0567	-0.2558	1.7272	0.1592	0.5115	0.0358	-0.0471	0.7969	0.0572	0.4528	37.6552	-0.131	31.9048
10	2.875	-1.1807	-0.282	6.6379	2.8437	7.1143	-0.1892	-0.3645	0.6435	0.2171	0.3536	-0.548	-1.053	0.5424	-0.1287	0.4007	-0.0857	-0.0326	0.443	0.0179	0.3831	28.857	5.9502	29.4509

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 64 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 84 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 85 through 90 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 91 through 125 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 8 through 33 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 34 through 43 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 44 through 65 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 66 through 84 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 85 through 127 )

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