PDB-4kgo: Crystal Structure of double Leucine to Methionine mutant human sp...

ID or keywords:

Entry

Database: PDB / ID: 4kgo

Title

Crystal Structure of double Leucine to Methionine mutant 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 /

SAD / Resolution: 3.194 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

-
Download

PDBx/mmCIF format	4kgo.cif.gz	155.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4kgo.ent.gz	128.9 KB	Display	PDB format
PDBx/mmJSON format	4kgo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4kgo_validation.pdf.gz	438.1 KB	Display	wwPDB validaton report
Full document	4kgo_full_validation.pdf.gz	444.8 KB	Display
Data in XML	4kgo_validation.xml.gz	15.7 KB	Display
Data in CIF	4kgo_validation.cif.gz	20.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kg/4kgo ftp://data.pdbj.org/pub/pdb/validation_reports/kg/4kgo	HTTPS FTP

-
Related structure data

Related structure data	4kghC C: citing same article (ref.)
Similar structure data	1m0z-d 5svq-d 5n2s-d 2aeo-1 2wac-d 6g3e-d 1u16-d 2reg-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#162 - Jun 2013 Dermcidin 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

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	151.827, 151.827, 35.943
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	75
Space group name H-M	P4

#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: 25122.059 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) / References: UniProt: Q9NP55
Sequence details	RESIDUE 105 IS AN ACCIDENTAL MUTATION

#1: Protein

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

Mass: 25122.059 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) / References: UniProt: Q9NP55

Sequence details

RESIDUE 105 IS AN ACCIDENTAL MUTATION

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.12 Å³/Da / Density % sol: 70.16 %
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

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.9794 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: 0.9794 Å / Relative weight: 1

Reflection

Redundancy: 14.5 % / Av σ(I) over netI: 24.94 / Number: 202585 / R_merge(I) obs: 0.109 / Χ²: 1 / D res high: 3.2 Å / D res low: 100 Å / Num. obs: 14004 / % possible obs: 99.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
8.68	100	98.6	1	0.069	2.172	13.9
6.89	8.68	99.7	1	0.075	1.673	15.7
6.02	6.89	100	1	0.095	1.33	16
5.47	6.02	100	1	0.104	1.136	16.2
5.08	5.47	100	1	0.101	1.082	16.1
4.78	5.08	100	1	0.099	1.113	16.3
4.54	4.78	100	1	0.1	1.102	16.1
4.34	4.54	100	1	0.115	1.085	16.4
4.18	4.34	100	1	0.137	0.894	16.4
4.03	4.18	100	1	0.171	0.879	16.3
3.91	4.03	100	1	0.212	0.779	16.2
3.79	3.91	100	1	0.265	0.748	15.9
3.69	3.79	100	1	0.296	0.715	16.1
3.6	3.69	100	1	0.355	0.709	15.1
3.52	3.6	98.7	1	0.396	0.673	13.6
3.45	3.52	99.6	1	0.531	0.692	12.8
3.38	3.45	99.6	1	0.565	0.658	11.7
3.31	3.38	98.4	1	0.626	0.652	10.4
3.26	3.31	95.9	1	0.717	0.657	9.2
3.2	3.26	90.8	1	0.759	0.575	7.8

Reflection

Resolution: 3.194→100 Å / Num. obs: 14004 / % possible obs: 99.1 % / Redundancy: 14.5 % / R_merge(I) obs: 0.109 / Net I/σ(I): 7.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
3.194-3.26	7.8	0.759	1	90.8
3.26-3.31	9.2	0.717	1	95.9
3.31-3.38	10.4	0.626	1	98.4
3.38-3.45	11.7	0.565	1	99.6
3.45-3.52	12.8	0.531	1	99.6
3.52-3.6	13.6	0.396	1	98.7
3.6-3.69	15.1	0.355	1	100
3.69-3.79	16.1	0.296	1	100
3.79-3.91	15.9	0.265	1	100
3.91-4.03	16.2	0.212	1	100
4.03-4.18	16.3	0.171	1	100
4.18-4.34	16.4	0.137	1	100
4.34-4.54	16.4	0.115	1	100
4.54-4.78	16.1	0.1	1	100
4.78-5.08	16.3	0.099	1	100
5.08-5.47	16.1	0.101	1	100
5.47-6.02	16.2	0.104	1	100
6.02-6.89	16	0.095	1	100
6.89-8.68	15.7	0.075	1	99.7
8.68-100	13.9	0.069	1	98.6

-
Phasing

Phasing	Method: SAD

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE		phasing
RESOLVE		phasing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 3.194→48.012 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.76 / σ(F): 1.35 / Phase error: 28.58 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2557	1299	5.02 %
R_work	0.2285	-	-
obs	0.2297	25870	97 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 110.913 Å² / k_sol: 0.324 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.3857 Å²	-0 Å²	0 Å²
2-	-	-10.3857 Å²	-0 Å²
3-	-	-	20.7714 Å²

Refinement step

Cycle: LAST / Resolution: 3.194→48.012 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2735	0	0	0	2735

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2764
X-RAY DIFFRACTION	f_angle_d	0.861	3777
X-RAY DIFFRACTION	f_dihedral_angle_d	13.201	975
X-RAY DIFFRACTION	f_chiral_restr	0.045	507
X-RAY DIFFRACTION	f_plane_restr	0.005	479

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 (%)
3.194-3.3215	0.3306	132	0.3257	2307	X-RAY DIFFRACTION	81
3.3215-3.4727	0.3674	148	0.3207	2645	X-RAY DIFFRACTION	96
3.4727-3.6557	0.3116	152	0.2895	2795	X-RAY DIFFRACTION	98
3.6557-3.8846	0.3291	145	0.2537	2794	X-RAY DIFFRACTION	100
3.8846-4.1844	0.2496	144	0.2267	2806	X-RAY DIFFRACTION	100
4.1844-4.6052	0.2247	140	0.1712	2811	X-RAY DIFFRACTION	100
4.6052-5.2709	0.2067	145	0.1892	2807	X-RAY DIFFRACTION	100
5.2709-6.638	0.2879	147	0.2786	2777	X-RAY DIFFRACTION	100
6.638-48.0173	0.228	146	0.2109	2829	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	3.9855	-4.1946	3.1121	4.5715	-1.4952	2.3937	0.3135	0.4848	0.86	-0.0976	-0.2889	-0.8117	0.0007	0.2323	0.0127	0.8102	0.0401	0.2724	0.9484	0.0872	1.2038	-45.8313	-91.2101	-2.2047
2	0.3735	2.5767	1.7682	2.1083	1.7627	7.6062	-0.2325	0.74	1.2582	-2.2433	0.0391	0.4304	-0.5409	-0.6437	0.7288	1.2864	0.0443	-0.0971	0.9804	0.0208	1.8999	-65.8186	-71.5456	-4.1662
3	6.3135	-3.7598	0.7926	4.6255	-1.1472	2.7045	-0.022	0.404	0.2454	0.9131	0.0992	-0.4917	0.2411	0.3833	-0.0856	0.5482	0.0364	0.2044	0.8839	0.0274	0.7562	-51.8304	-90.7321	1.1909
4	3.9569	-3.9684	-3.5335	7.7444	5.8696	8.3516	0.4562	0.6364	-0.355	-0.9705	-0.2608	0.1059	-0.0116	0.5254	-0.0649	0.9639	0.2725	0.0786	1.1126	-0.0219	1.0722	-48.3069	-99.2732	-9.9781
5	3.5961	-2.5607	1.8131	6.6177	-2.8317	0.5541	0.512	0.7823	-0.427	-0.6387	-0.8609	0.3853	0.5323	0.2297	0.3884	0.8428	0.1645	0.0678	1.061	0.0745	0.7657	-51.7621	-96.4843	-4.0283
6	8.7318	-5.6284	0.9019	3.5778	-0.5871	0.8017	0.1701	0.4491	1.519	-0.156	-0.4634	-0.3944	-0.1777	0.6259	0.3046	1.1113	0.2001	0.23	1.1436	0.0272	1.431	-14.0012	-116.7133	2.7771
7	7.6932	-1.2923	1.2362	-1.0622	-3.2911	0.7124	0.8258	1.7063	1.2407	0.5862	-0.4603	-0.1117	0.1751	0.6204	0.0269	1.392	0.2116	0.0932	1.2239	-0.2026	2.1045	-2.6255	-119.9551	2.644
8	4.9098	0.5565	-1.0526	4.1656	-3.2942	8.7925	-0.3603	-2.265	-0.3657	-0.1485	0.6424	1.2964	0.3442	-0.5914	-1.4663	1.2871	0.2805	0.1524	1.0639	0.1443	1.9148	-33.8572	-125.75	9.6571
9	7.975	3.6517	0.3644	1.5713	-0.145	0.4304	0.4217	1.1867	1.2653	-0.2325	-0.475	0.3584	-0.0515	0.4731	-0.2745	1.3439	0.3759	0.0392	1.6403	-0.2067	1.8597	-3.0859	-121.4449	-2.5795
10	5.1658	1.7909	0.0565	0.3625	0.1181	2.6262	0.2716	0.5976	-1.1737	0.0149	-0.2763	0.107	-0.0754	0.474	0.2171	1.2132	0.3831	0.0375	1.0093	0.0184	0.9293	-17.0317	-122.3833	1.9813

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resseq 34:96)
2	X-RAY DIFFRACTION	2	chain 'B' and (resseq 97:106)
3	X-RAY DIFFRACTION	3	chain 'B' and (resseq 107:149)
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 150:177)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 178:255)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 43:141)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 142:166)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 167:177)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 178:197)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 198:254)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi