PDB-5tng: Crystal structure of the E153Q mutant of the CFTR inhibitory fact...

ID or keywords:

Entry

Database: PDB / ID: 5tng

Title

Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 14,15-EpETE hydrolysis intermediate

Components

CFTR inhibitory factor

Keywords

HYDROLASE / epoxide hydrolase / hydroxyalkyl-enzyme intermediate

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Hvorecny, K.L. / Madden, D.R.

Funding support

United States, 9items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI091699	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM113132	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM106394	United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	DK097154	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM008704	United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	ES002710	United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	ES004699	United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	ES024806	United States
Cystic Fibrosis Foundation	STANTO19R0	United States

Citation

Journal: Structure / Year: 2017
Title: Active-Site Flexibility and Substrate Specificity in a Bacterial Virulence Factor: Crystallographic Snapshots of an Epoxide Hydrolase.
Authors: Hvorecny, K.L. / Bahl, C.D. / Kitamura, S. / Lee, K.S.S. / Hammock, B.D. / Morisseau, C. / Madden, D.R.

History

Deposition	Oct 14, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Database references / Category: pdbx_database_related
Revision 1.2	Mar 23, 2022	Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5tng.cif.gz	497.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5tng.ent.gz	408.3 KB	Display	PDB format
PDBx/mmJSON format	5tng.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5tng_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	5tng_full_validation.pdf.gz	1.3 MB	Display
Data in XML	5tng_validation.xml.gz	55.9 KB	Display
Data in CIF	5tng_validation.cif.gz	82.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tn/5tng ftp://data.pdbj.org/pub/pdb/validation_reports/tn/5tng	HTTPS FTP

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Related structure data

Related structure data	5tndC 5tneC 5tnfC 5tnhC 5tniC 5tnjC 5tnkC 5tnlC 5tnmC 5tnnC 5tnpC 5tnqC 5tnrC 5tnsC 3kd2S 4dmc S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5tnn-1 6kxr-2 3kd2-2 4eus-2 5tnr-2 5tni-1 5k3e-d 4yx9-1 3r41-d 7clz-2 6kxr-1 6gxt-d 5tnr-1 5tnq-2 5nyv-d 4dno-1 4dnf-2 5k3b-d 4dno-2 5o2i-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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: CFTR inhibitory factor

B: CFTR inhibitory factor

C: CFTR inhibitory factor

D: CFTR inhibitory factor

hetero molecules

138 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CFTR inhibitory factor

B: CFTR inhibitory factor

hetero molecules

defined by author&software
69 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: CFTR inhibitory factor

D: CFTR inhibitory factor

hetero molecules

defined by author&software
69 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	169.09, 83.522, 89.915
Angle α, β, γ (deg.)	90.00, 100.17, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	D-782- HOH
2	1	D-819- HOH

#1: Protein	CFTR inhibitory factor Mass: 34163.715 Da / Num. of mol.: 4 / Mutation: E153Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: PA14_26090 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS
#2: Chemical	ChemComp-7LE / (5Z,8Z,11Z,14R,15R,17Z)-14,15-dihydroxyicosa-5,8,11,17-tetraenoic acid Mass: 336.466 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₃₂O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1231 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.29 Å³/Da / Density % sol: 46.21 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: sodium acetate, pH5 calcium chloride PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8856 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8856 Å / Relative weight: 1
Reflection	Resolution: 1.75→19.93 Å / Num. obs: 123855 / % possible obs: 99.9 % / Redundancy: 5.75 % / R_merge(I) obs: 0.114 / Net I/σ(I): 14.6
Reflection shell	Resolution: 1.75→1.85 Å / Redundancy: 5.73 % / R_merge(I) obs: 0.636 / Mean I/σ(I) obs: 3.08 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS	NOVEMBER 1, 2011	data reduction
XDS	NOVEMBER 1, 2011	data scaling
PHENIX	2.3.0	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2

Resolution: 1.75→19.93 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.96

	R_factor	Num. reflection	% reflection
R_free	0.1808	6220	5.02 %
R_work	0.1499	-	-
obs	0.1514	123848	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.75→19.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9416	0	92	1231	10739

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9960
X-RAY DIFFRACTION	f_angle_d	0.843	13540
X-RAY DIFFRACTION	f_dihedral_angle_d	15.743	5917
X-RAY DIFFRACTION	f_chiral_restr	0.054	1393
X-RAY DIFFRACTION	f_plane_restr	0.007	1774

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 (%)
1.75-1.7699	0.218	311	0.1939	3747	X-RAY DIFFRACTION	100
1.7699-1.7907	10000000	0	0.1868	4085	X-RAY DIFFRACTION	100
1.7907-1.8125	0.2455	311	0.1883	3865	X-RAY DIFFRACTION	100
1.8125-1.8354	0.2543	311	0.19	3784	X-RAY DIFFRACTION	100
1.8354-1.8596	10000000	0	0.1966	4103	X-RAY DIFFRACTION	100
1.8596-1.885	0.2377	311	0.1867	3777	X-RAY DIFFRACTION	100
1.885-1.9119	0.2222	311	0.1732	3827	X-RAY DIFFRACTION	100
1.9119-1.9405	10000000	0	0.1631	4079	X-RAY DIFFRACTION	100
1.9405-1.9707	0.2004	311	0.16	3807	X-RAY DIFFRACTION	100
1.9707-2.003	0.1846	311	0.1587	3825	X-RAY DIFFRACTION	100
2.003-2.0375	10000000	0	0.1557	4118	X-RAY DIFFRACTION	100
2.0375-2.0745	0.1937	311	0.1542	3763	X-RAY DIFFRACTION	100
2.0745-2.1144	0.1969	311	0.1555	3805	X-RAY DIFFRACTION	100
2.1144-2.1575	10000000	0	0.1509	4174	X-RAY DIFFRACTION	100
2.1575-2.2044	0.1953	311	0.153	3785	X-RAY DIFFRACTION	100
2.2044-2.2556	0.1887	311	0.1468	3847	X-RAY DIFFRACTION	100
2.2556-2.3119	10000000	0	0.1503	4078	X-RAY DIFFRACTION	100
2.3119-2.3743	0.1865	311	0.1466	3815	X-RAY DIFFRACTION	100
2.3743-2.4441	0.1975	311	0.1553	3806	X-RAY DIFFRACTION	100
2.4441-2.5228	10000000	0	0.1559	4125	X-RAY DIFFRACTION	100
2.5228-2.6128	0.1801	311	0.147	3850	X-RAY DIFFRACTION	100
2.6128-2.7171	0.182	311	0.1511	3800	X-RAY DIFFRACTION	100
2.7171-2.8405	10000000	0	0.1475	4129	X-RAY DIFFRACTION	100
2.8405-2.9898	0.1753	311	0.154	3847	X-RAY DIFFRACTION	100
2.9898-3.1764	0.1788	311	0.1526	3798	X-RAY DIFFRACTION	100
3.1764-3.4205	10000000	0	0.1428	4190	X-RAY DIFFRACTION	100
3.4205-3.7626	0.156	311	0.134	3837	X-RAY DIFFRACTION	100
3.7626-4.3023	0.124	311	0.1279	3852	X-RAY DIFFRACTION	100
4.3023-5.4025	10000000	0	0.1156	4182	X-RAY DIFFRACTION	100
5.4025-19.9308	0.1621	311	0.1437	3928	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	0.712	0.0877	0.0944	0.6106	0.039	0.6309	0.0126	0.0826	-0.088	-0.0567	0.0028	-0.0635	0.0865	0.05	-0.0061	0.0819	0.0013	-0.0035	0.0818	-0.0164	0.0681	21.819	12.3965	-27.5848
2	0.9564	0.3564	0.0165	0.9817	0.1247	0.5004	-0.0217	0.0038	0.143	0.0134	0.0179	-0.0171	-0.0885	0.009	-0.0001	0.0863	-0.0114	-0.0183	0.0683	0.0002	0.0994	31.011	51.5389	-15.7225
3	0.7283	0.0077	-0.0021	0.8269	-0.0718	0.7448	0.0129	0.0506	0.1482	-0.053	-0.015	0.0985	-0.0993	-0.0548	0.0006	0.0814	0.0018	-0.0056	0.0742	0.0086	0.1141	-5.9353	44.7843	-27.2481
4	0.9854	0.2238	-0.0727	0.652	-0.0687	0.4696	-0.0055	-0.0302	-0.0813	-0.0065	-0.0136	0.0535	0.0524	0.0104	0.0179	0.083	-0.0223	0.0032	0.08	0.0008	0.0628	-15.0475	5.3452	-15.747

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 25:320 )	A	25 - 320
2	X-RAY DIFFRACTION	2	( CHAIN B AND RESID 25:318 )	B	25 - 318
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 25:317 )	C	25 - 317
4	X-RAY DIFFRACTION	4	( CHAIN D AND RESID 25:321 )	D	25 - 321

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