PDB-4kgh: Crystal Structure of human splunc1 lacking the secretion signal s...

ID or keywords:

Entry

Database: PDB / ID: 4kgh

Title

Crystal Structure of human splunc1 lacking the secretion signal sequence

Components

BPI fold-containing family A member 1

Keywords

IMMUNE SYSTEM / beta barrel / BPI-like fold

Function / homology

Function and homology information

immune response in nasopharyngeal-associated lymphoid tissue / regulation of sodium ion transmembrane transport / negative regulation of single-species biofilm formation in or on host organism / multicellular organismal-level water homeostasis / surfactant homeostasis / Antimicrobial peptides / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to virus / innate immune response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.806 Å

Authors

Betts, L. / Walton, W.G.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular basis for pH-dependent mucosal dehydration in cystic fibrosis airways.
Authors: Garland, A.L. / Walton, W.G. / Coakley, R.D. / Tan, C.D. / Gilmore, R.C. / Hobbs, C.A. / Tripathy, A. / Clunes, L.A. / Bencharit, S. / Stutts, M.J. / Betts, L. / Redinbo, M.R. / Tarran, R.

History

Deposition	Apr 29, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 25, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4kgh.cif.gz	153 KB	Display	PDBx/mmCIF format
PDB format	pdb4kgh.ent.gz	127.7 KB	Display	PDB format
PDBx/mmJSON format	4kgh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4kgh_validation.pdf.gz	468.8 KB	Display	wwPDB validaton report
Full document	4kgh_full_validation.pdf.gz	479 KB	Display
Data in XML	4kgh_validation.xml.gz	16.6 KB	Display
Data in CIF	4kgh_validation.cif.gz	21.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kg/4kgh ftp://data.pdbj.org/pub/pdb/validation_reports/kg/4kgh	HTTPS FTP

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Related structure data

Related structure data	4kgoC C: citing same article (ref.)
Similar structure data	5svs-d 6xvi-1 5yve-d 6d52-d 1l8d-d 5svj-d 6ixy-4 5svr-d 6jq5-d 6ixy-2 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	#162 - Jun 2013 Dermcidin similarity (1) #135 - Mar 2011 Integrase similarity (1) #193 - Jan 2016 Siderocalin similarity (1)

Deposited unit

B: BPI fold-containing family A member 1

A: BPI fold-containing family A member 1

hetero molecules

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

1

Idetical with deposited unit
defined by software

2

B: BPI fold-containing family A member 1

hetero molecules

A: BPI fold-containing family A member 1

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

Unit cell

Length a, b, c (Å)	47.475, 203.727, 118.612
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

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Protein , 1 types, 2 molecules BA

#1: Protein	BPI fold-containing family A member 1 / Lung-specific protein X / Nasopharyngeal carcinoma-related protein / Palate lung and nasal ...Lung-specific protein X / Nasopharyngeal carcinoma-related protein / Palate lung and nasal epithelium clone protein / Secretory protein in upper respiratory tracts / Tracheal epithelium-enriched protein / Von Ebner protein Hl Mass: 24945.297 Da / Num. of mol.: 2 / Fragment: UNP residues 19-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BPIFA1, LUNX, NASG, PLUNC, SPURT, UNQ787/PRO1606 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)codon plus RIPL / References: UniProt: Q9NP55

#1: Protein

BPI fold-containing family A member 1 / Lung-specific protein X / Nasopharyngeal carcinoma-related protein / Palate lung and nasal ...

Mass: 24945.297 Da / Num. of mol.: 2 / Fragment: UNP residues 19-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: BPIFA1, LUNX, NASG, PLUNC, SPURT, UNQ787/PRO1606 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)codon plus RIPL / References: UniProt: Q9NP55

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Non-polymers , 5 types, 12 molecules

#2: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO₃
#3: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₄N
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	RESIDUE 105 IS AN ACCIDENTAL MUTATION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.87 Å³/Da / Density % sol: 57.21 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: 8% PEG 400, .2 M tri-sodium citrate, .1 M Tris-HCl pH 8.5, vapor diffusion, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1 Å

Detector

Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2012

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.8→100 Å / Num. obs: 13819 / % possible obs: 95.8 % / Redundancy: 6.5 % / R_merge(I) obs: 0.092 / Χ²: 2.757 / Net I/σ(I): 12

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.8-2.85	4.4	0.379	499	1.25	1	72.5
2.85-2.9	4.7	0.334	550	1.353	1	77.5
2.9-2.96	5.1	0.344	603	1.443	1	83.8
2.96-3.02	5.5	0.328	635	1.465	1	93.5
3.02-3.08	5.8	0.312	689	1.472	1	96.6
3.08-3.15	6.3	0.287	718	1.444	1	97.4
3.15-3.23	6.6	0.233	692	1.656	1	99.6
3.23-3.32	6.7	0.211	699	1.954	1	100
3.32-3.42	6.9	0.188	720	2.081	1	99
3.42-3.53	6.9	0.169	699	2.367	1	100
3.53-3.65	7	0.169	730	2.651	1	100
3.65-3.8	7.1	0.142	697	2.814	1	99.7
3.8-3.97	7	0.125	734	4.051	1	99.6
3.97-4.18	7.2	0.108	702	3.623	1	99.6
4.18-4.44	7	0.09	716	3.887	1	99.3
4.44-4.79	6.8	0.076	726	3.944	1	98.8
4.79-5.27	7.1	0.076	728	3.415	1	99.2
5.27-6.03	7.1	0.08	733	3.398	1	99.9
6.03-7.6	7.2	0.068	746	3.473	1	99.9
7.6-100	6.3	0.053	803	4.003	1	98.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
RESOLVE		phasing
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.806→38.639 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.6818 / SU ML: 0.43 / σ(F): 1.34 / Phase error: 36.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2952	1374	9.99 %
R_work	0.2458	-	-
obs	0.2507	13752	94.44 %

Solvent computation

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

Displacement parameters

B_iso max: 147.47 Å² / B_iso mean: 74.7266 Å² / B_iso min: 32.87 Å²

Refinement step

Cycle: LAST / Resolution: 2.806→38.639 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2754	0	12	8	2774

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2801
X-RAY DIFFRACTION	f_angle_d	0.854	3827
X-RAY DIFFRACTION	f_chiral_restr	0.041	512
X-RAY DIFFRACTION	f_plane_restr	0.005	485
X-RAY DIFFRACTION	f_dihedral_angle_d	17.677	983

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.8064-2.9067	0.3942	91	0.307	824	915	64
2.9067-3.023	0.4306	126	0.3115	1122	1248	87
3.023-3.1605	0.3685	138	0.3065	1260	1398	97
3.1605-3.3271	0.3202	139	0.2782	1260	1399	99
3.3271-3.5354	0.3534	143	0.2602	1288	1431	99
3.5354-3.8082	0.2971	143	0.2531	1293	1436	100
3.8082-4.191	0.2987	145	0.2256	1294	1439	99
4.191-4.7965	0.2574	145	0.1988	1314	1459	99
4.7965-6.0393	0.2971	148	0.2442	1324	1472	100
6.0393-38.6423	0.2551	156	0.2483	1399	1555	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	4.0394	-0.0313	1.1609	2.4644	-1.4436	2.1002	0.2653	-0.0776	-0.4625	-1.6211	-0.0737	0.5813	0.6091	0.8965	-0.1546	0.5556	0.0127	0.1147	0.5295	-0.0133	0.2646	15.182	31.4875	-15.3097
2	-0.4582	-0.2488	-0.66	2.048	6.796	4.5184	0.6141	2.6769	0.0638	-1.8743	0.6469	-0.2229	-0.6219	0.0983	-0.654	1.188	0.0325	-0.0421	0.8294	0.3125	0.9997	12.826	57.2546	-18.4756
3	1.6579	-0.3976	2.0819	2.4597	-0.1569	2.4512	-0.5481	-0.1058	-0.8136	-0.3901	0.9566	0.002	-0.5402	-0.5389	0.0835	1.131	0.0782	0.0542	1.0717	0.3824	1.0323	15.185	74.0293	-20.4369
4	1.2592	3.0887	-2.0609	5.3507	-4.4043	3.2242	0.1738	0.1257	1.1608	-0.1314	0.8096	0.6823	-0.2893	1.0396	-0.5372	0.882	-0.0722	0.1512	0.6674	0.0106	0.8643	21.9075	62.4711	-17.0286
5	0.232	0.0573	-0.6071	5.1652	1.1224	2.0727	-0.07	0.0874	0.3786	-0.5158	0.1125	0.122	0.0824	0.1247	-0.081	0.3678	0.0586	-0.0687	0.3844	0.0205	0.4512	12.2322	42.9389	-9.0132
6	3.5198	-0.2657	-2.1688	0.2058	0.2865	2.1613	0.347	0.1439	-0.933	-0.46	0.1003	0.2202	1.2855	-0.4277	-0.346	0.9897	0.0065	-0.2099	0.4526	0.134	0.6361	-1.0373	32.5489	-18.7048
7	2.8545	0.3186	0.9599	4.8589	1.2091	3.0919	-0.089	-0.1929	0.6463	-0.5431	-0.2887	0.2855	-0.0857	0.0148	0.3221	0.4127	-0.0104	0.04	0.4309	0.0065	0.4447	12.151	52.2999	-8.2036
8	6.2988	0.1471	-0.7705	5.1052	0.2666	5.6773	-0.2973	0.3261	-0.4401	-1.2492	0.0141	0.7025	0.569	-0.5466	0.4804	0.7496	-0.043	-0.1994	0.4063	-0.0204	0.7311	2.4464	20.3565	-14.2139
9	3.5995	-1.6804	0.4022	4.4309	-0.2691	0.682	-0.2031	0.2417	0.6544	0.0301	-0.0464	-0.9567	0.0087	0.1787	0.0872	0.4664	0.0344	-0.062	0.5678	-0.0291	0.4982	24.3885	1.4007	-11.9571
10	0.4951	-0.7503	-0.5566	1.2232	0.37	0.3215	0.2317	0.2855	1.0597	1.8881	-0.0064	-0.0864	0.7291	0.6359	0.002	1.4435	0.3486	-0.0763	0.9081	0.007	0.9377	43.369	-27.4112	-8.6997
11	5.9296	-3.0942	-0.3886	4.5354	-0.2	3.2382	1.0091	1.062	0.2574	-1.8919	-0.956	0.0748	0.3284	-0.0578	0.0756	0.8628	-0.0366	-0.4413	0.3309	-0.0848	0.3961	19.7112	-1.038	-17.5599
12	2.6291	-1.3289	-0.0641	5.3045	-0.456	3.4438	0.2511	0.614	-0.1802	-0.5432	-0.0075	-0.1751	0.1454	0.3942	-0.1457	0.4357	0.056	-0.1114	0.4754	-0.1146	0.4353	24.5522	-7.1318	-16.8706
13	0.3423	0.3424	-1.1932	0.1072	-0.4251	4.356	-1.3776	0.7468	0.0436	0.9626	0.7775	1.5398	-1.6568	-2.1878	-0.3501	0.8567	0.4499	0.2086	0.8208	0.0363	0.7311	2.9033	5.0699	1.6672
14	2.1654	-1.8781	-0.0416	2.8489	-0.5902	0.8703	0.1055	0.2591	-0.4473	-0.629	-0.2362	0.3321	0.2793	-0.0932	-0.0205	0.7889	0.1132	-0.1094	0.5311	0.0009	0.5882	17.7386	-4.1973	-13.774

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 43 through 69 )	B
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 70 through 89 )	B
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 90 through 99 )	B
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 100 through 111 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 112 through 165 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 166 through 182 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 183 through 231 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 232 through 254 )	B
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 43 through 91 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 92 through 106 )	A
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 107 through 127 )	A
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 128 through 167 )	A
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 168 through 176 )	A
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 177 through 254 )	A

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