PDB-5ni4: Crystal structure of human LTA4H mutant E271A in complex with LTA...

ID or keywords:

Entry

Database: PDB / ID: 5ni4

Title

Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form II)

Components

Leukotriene A-4 hydrolase

Keywords

HYDROLASE / Metallopeptidase / epoxide hydrolase / leukotriene A4

Function / homology

Function and homology information

leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / Biosynthesis of protectins / protein metabolic process / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.895 Å

Authors

Stsiapanava, A.

Funding support

Sweden, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Capturing LTA4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis.
Authors: Stsiapanava, A. / Samuelsson, B. / Haeggstrom, J.Z.

History

Deposition	Mar 23, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 23, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Sep 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ni4.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5ni4.ent.gz	930.6 KB	Display	PDB format
PDBx/mmJSON format	5ni4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ni/5ni4 ftp://data.pdbj.org/pub/pdb/validation_reports/ni/5ni4	HTTPS FTP

-
Related structure data

Related structure data	4dprC 5ni2SC 5ni6C 5niaC 5nidC 5nieC 4ms6 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6o5h-d 4l08-d 5xa1-1 3hty-d 2fug-4 4fzh-d 2fug-1 5khn-d 3i9v-1 1ykj-2 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	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Leukotriene A-4 hydrolase

B: Leukotriene A-4 hydrolase

C: Leukotriene A-4 hydrolase

hetero molecules

212 kDa, 3 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)	139.560, 139.560, 87.950
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Leukotriene A-4 hydrolase / LTA-4 hydrolase / Leukotriene A(4) hydrolase Mass: 70134.820 Da / Num. of mol.: 3 / Mutation: E271A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Plasmid: pT3MB4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P09960, leukotriene-A4 hydrolase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₅N₂
#4: Chemical	ChemComp-DJ3 / 5S-5,6-oxido-7,9-trans-11,14-cis-eicosatetraenoic acid Mass: 318.450 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₀H₃₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2056 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.57 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 8% (w/v) PEG 20 000, 15% (w/v) PEG MME 550, 100 mM MES/imidazole pH 6.9, 20 mM of each alcohol (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol) PH range: 6.9

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.895→49.81 Å / Num. obs: 152082 / % possible obs: 99.93 % / Redundancy: 6.4 % / B_iso Wilson estimate: 22.08 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.1885 / R_pim(I) all: 0.08085 / Net I/σ(I): 6.61
Reflection shell	Resolution: 1.895→1.963 Å / Redundancy: 6.3 % / R_merge(I) obs: 1.609 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 15217 / CC_1/2: 0.351 / R_pim(I) all: 0.6945 / % possible all: 99.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NI2

5ni2

Resolution: 1.895→49.807 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2	8107	5.33 %
R_work	0.1615	-	-
obs	0.1636	152057	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.895→49.807 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14562	0	107	2056	16725

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	15519
X-RAY DIFFRACTION	f_angle_d	0.844	21095
X-RAY DIFFRACTION	f_dihedral_angle_d	17.503	5847
X-RAY DIFFRACTION	f_chiral_restr	0.048	2339
X-RAY DIFFRACTION	f_plane_restr	0.005	2709

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 (%)
1.8952-1.9167	0.3642	266	0.3231	4789	X-RAY DIFFRACTION	99
1.9167-1.9392	0.3484	272	0.3116	4821	X-RAY DIFFRACTION	100
1.9392-1.9629	0.3302	264	0.2815	4795	X-RAY DIFFRACTION	100
1.9629-1.9877	0.3185	280	0.2682	4800	X-RAY DIFFRACTION	100
1.9877-2.0139	0.3054	272	0.2483	4709	X-RAY DIFFRACTION	100
2.0139-2.0415	0.2543	266	0.2392	4835	X-RAY DIFFRACTION	100
2.0415-2.0707	0.2531	263	0.234	4747	X-RAY DIFFRACTION	100
2.0707-2.1016	0.2682	275	0.2274	4849	X-RAY DIFFRACTION	100
2.1016-2.1344	0.274	272	0.2159	4794	X-RAY DIFFRACTION	100
2.1344-2.1694	0.2396	282	0.2091	4828	X-RAY DIFFRACTION	100
2.1694-2.2068	0.2623	246	0.208	4802	X-RAY DIFFRACTION	100
2.2068-2.2469	0.2538	281	0.2106	4823	X-RAY DIFFRACTION	100
2.2469-2.2902	0.2688	254	0.205	4777	X-RAY DIFFRACTION	100
2.2902-2.3369	0.2157	279	0.1769	4806	X-RAY DIFFRACTION	100
2.3369-2.3877	0.2166	272	0.1729	4789	X-RAY DIFFRACTION	100
2.3877-2.4433	0.2169	264	0.1687	4788	X-RAY DIFFRACTION	100
2.4433-2.5043	0.2207	260	0.1664	4836	X-RAY DIFFRACTION	100
2.5043-2.5721	0.2028	268	0.1641	4792	X-RAY DIFFRACTION	100
2.5721-2.6477	0.2018	291	0.1502	4775	X-RAY DIFFRACTION	100
2.6477-2.7332	0.1974	257	0.1462	4852	X-RAY DIFFRACTION	100
2.7332-2.8309	0.1929	269	0.1461	4750	X-RAY DIFFRACTION	100
2.8309-2.9442	0.1931	295	0.1451	4822	X-RAY DIFFRACTION	100
2.9442-3.0782	0.2003	258	0.1476	4774	X-RAY DIFFRACTION	100
3.0782-3.2404	0.1849	276	0.1436	4808	X-RAY DIFFRACTION	100
3.2404-3.4434	0.1719	285	0.1405	4791	X-RAY DIFFRACTION	100
3.4434-3.7092	0.1854	285	0.1345	4746	X-RAY DIFFRACTION	100
3.7092-4.0823	0.1492	279	0.1298	4838	X-RAY DIFFRACTION	100
4.0823-4.6727	0.1416	248	0.1099	4812	X-RAY DIFFRACTION	100
4.6727-5.8856	0.1537	256	0.1185	4815	X-RAY DIFFRACTION	100
5.8856-49.8242	0.1757	272	0.1649	4787	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	0.217	-0.0337	-0.0789	0.4398	-0.0461	0.4534	0.0095	0.051	-0.0021	-0.1204	0.0144	-0.0412	-0.1332	0.0688	0	0.247	-0.0204	0.0041	0.1825	0.0038	0.2253	-1.0169	21.8693	-11.1124
2	0.4042	-0.0639	-0.032	0.2467	0.1754	0.4807	-0.0006	-0.0171	-0.0186	0.0395	-0.0227	0.027	0.0006	-0.0603	0	0.177	0.0084	0.0006	0.1674	0.0036	0.2098	-16.5836	13.146	9.8759
3	0.1596	-0.0159	-0.0354	0.4988	0.3609	0.3968	-0.035	-0.1131	0.0279	0.1138	0.0735	0.0428	-0.201	0.0281	0.0016	0.2936	0.0359	0.0033	0.2016	-0.0252	0.2154	-8.9941	31.0275	27.6865
4	0.3622	-0.1597	0.2478	0.3234	-0.1868	0.475	-0.0218	-0.131	0.0282	-0.018	0.0141	-0.0423	0.0761	0.0393	0.0016	0.1688	0.0427	0.0048	0.2067	0.0119	0.2	15.5153	64.7706	-5.4531
5	0.1784	0.0841	-0.1348	0.2364	-0.1349	0.3958	-0.0023	0.0005	0.0237	-0.0581	-0.0092	-0.0135	0.1141	-0.035	-0.0001	0.2388	-0.009	0.0008	0.1709	0.0098	0.19	-1.7776	59.7246	-26.505
6	0.3839	-0.0874	-0.1199	0.3028	-0.0797	0.2273	-0.0632	0.0564	-0.0395	-0.19	0.0081	-0.0701	0.1691	0.0498	-0.0006	0.4164	0.0563	0.074	0.2231	-0.0036	0.2474	16.4305	53.2137	-44.4656
7	0.539	-0.1315	-0.0803	0.3848	-0.2511	0.3273	-0.0018	0.1477	0.0408	-0.0871	0.0023	-0.0128	-0.0793	-0.016	-0	0.2495	0.0158	-0.0071	0.1934	0.03	0.198	58.7741	59.5234	-19.9433
8	0.5231	0.0504	0.1162	0.1181	0.0383	0.4289	-0.0195	-0.0527	-0.0417	0.0121	0.0227	0.0113	-0.0268	-0.0486	-0	0.174	0.0185	-0.0019	0.1896	0.0207	0.1923	49.4598	44.1792	0.8624
9	0.4592	-0.1713	-0.161	0.2993	0.1959	0.4763	-0.0422	-0.2523	0.1112	0.054	0.0799	-0.0369	-0.1954	-0.1996	0.0659	0.3077	0.1136	-0.0021	0.3532	-0.0396	0.2139	47.6673	63.5141	18.6823

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resi 3:209
2	X-RAY DIFFRACTION	2	chain A and resi 210:465
3	X-RAY DIFFRACTION	3	chain A and resi 466:609
4	X-RAY DIFFRACTION	4	chain B and resi 2:209
5	X-RAY DIFFRACTION	5	chain B and resi 210:465
6	X-RAY DIFFRACTION	6	chain B and resi 466:609
7	X-RAY DIFFRACTION	7	chain C and resi 2:209
8	X-RAY DIFFRACTION	8	chain C and resi 210:465
9	X-RAY DIFFRACTION	9	chain C and resi 466:609

-
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

-
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

-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

-
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