PDB-6bnd: Crystal structure of the intrinsic colistin resistance enzyme ICR...

ID or keywords:

Entry

Database: PDB / ID: 6bnd

Title

Crystal structure of the intrinsic colistin resistance enzyme ICR(Mc) from Moraxella catarrhalis, catalytic domain, Thr315Ala mutant mono-zinc and phosphoethanolamine complex

Components

Phosphoethanolamine transferase

Keywords

TRANSFERASE /

antibiotic resistance / colistin /

polymyxin / phosphoethanolamine transferase / sulfatase fold / alpha/beta protein /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

transferase activity, transferring phosphorus-containing groups / sulfuric ester hydrolase activity /

plasma membrane
Similarity search - Function

Biological species

Moraxella sp. HMSC061H09 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.66 Å

Authors

Stogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Savchenko, A. / Anderson, W.F. / Satchell, K.J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201200026C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201200060C	United States

Citation

Journal: ACS Chem. Biol. / Year: 2018
Title: Substrate Recognition by a Colistin Resistance Enzyme from Moraxella catarrhalis.
Authors: Stogios, P.J. / Cox, G. / Zubyk, H.L. / Evdokimova, E. / Wawrzak, Z. / Wright, G.D. / Savchenko, A.

History

Deposition	Nov 16, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2018	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Apr 25, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	May 30, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 2023	Group: Data collection / Database references ...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 / 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.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	6bnd.cif.gz	308.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6bnd.ent.gz	241.9 KB	Display	PDB format
PDBx/mmJSON format	6bnd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bn/6bnd ftp://data.pdbj.org/pub/pdb/validation_reports/bn/6bnd	HTTPS FTP

-
Related structure data

Related structure data	6bncC 6bneSC 6bnfC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1fin-1 3qhw-1 1okw-2 6bnc-d 2cjm-2 2uue-1 3qhr-2 3qhw-2 3bhv-1 1ol2-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP-95742

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Phosphoethanolamine transferase

B: Phosphoethanolamine transferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.520, 155.240, 66.410
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-1198- HOH

-
Protein , 1 types, 2 molecules AB

#1: Protein	Phosphoethanolamine transferase Mass: 37941.348 Da / Num. of mol.: 2 / Mutation: T315A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moraxella sp. HMSC061H09 (bacteria) / Gene: HMPREF2573_04170 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A0A1E9VP98

#1: Protein

Phosphoethanolamine transferase

Mass: 37941.348 Da / Num. of mol.: 2 / Mutation: T315A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Moraxella sp. HMSC061H09 (bacteria) / Gene: HMPREF2573_04170 / Plasmid: pMCSG53 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A0A1E9VP98

-
Non-polymers , 5 types, 1081 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID / Phosphorylethanolamine Mass: 141.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₈NO₄P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol Mass: 1529.829 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆₉H₁₄₀O₃₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1073 / 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: 2.53 Å³/Da / Density % sol: 51.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES pH 6, 22% (w/v) PEG 400, 2.5 mM zinc chloride, 5 mM phosphoethanolamine. Cryoprotectant paratone.

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27687 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 20, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.27687 Å / Relative weight: 1
Reflection	Resolution: 1.64→31.8 Å / Num. obs: 91550 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.18 / R_pim(I) all: 0.044 / Net I/σ(I): 14.5
Reflection shell	Resolution: 1.64→1.68 Å / Redundancy: 12.6 % / R_merge(I) obs: 1.95 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6896 / CC_1/2: 0.594 / R_pim(I) all: 0.827 / % possible all: 99.3

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_2733: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX	phenix.phaser	phasing
PHENIX	phenix.autobuild	model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6BNE

6bne

Resolution: 1.66→31.8 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.65

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1922	3712	2.11 %	RANDOM
R_work	0.1508	-	-	-
obs	0.1517	175556	99.83 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.66→31.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5186	0	55	1073	6314

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	5440
X-RAY DIFFRACTION	f_angle_d	1.319	7420
X-RAY DIFFRACTION	f_dihedral_angle_d	17.86	1995
X-RAY DIFFRACTION	f_chiral_restr	0.097	825
X-RAY DIFFRACTION	f_plane_restr	0.009	974

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 (%)
1.66-1.681	0.3267	135	0.342	6323	X-RAY DIFFRACTION	100
1.681-1.7031	0.327	136	0.3208	6407	X-RAY DIFFRACTION	100
1.7031-1.7265	0.3544	136	0.3043	6323	X-RAY DIFFRACTION	100
1.7265-1.7511	0.3097	138	0.2777	6373	X-RAY DIFFRACTION	100
1.7511-1.7773	0.273	136	0.2677	6388	X-RAY DIFFRACTION	100
1.7773-1.805	0.251	137	0.2533	6302	X-RAY DIFFRACTION	100
1.805-1.8346	0.2637	139	0.2451	6415	X-RAY DIFFRACTION	100
1.8346-1.8662	0.2543	137	0.2236	6346	X-RAY DIFFRACTION	100
1.8662-1.9002	0.24	139	0.2027	6395	X-RAY DIFFRACTION	100
1.9002-1.9367	0.2347	132	0.1882	6317	X-RAY DIFFRACTION	100
1.9367-1.9762	0.2034	139	0.1726	6415	X-RAY DIFFRACTION	100
1.9762-2.0192	0.1923	140	0.1678	6324	X-RAY DIFFRACTION	100
2.0192-2.0662	0.2145	140	0.1597	6410	X-RAY DIFFRACTION	100
2.0662-2.1178	0.2246	134	0.1621	6317	X-RAY DIFFRACTION	100
2.1178-2.1751	0.2066	143	0.1598	6396	X-RAY DIFFRACTION	100
2.1751-2.2391	0.1935	141	0.1398	6315	X-RAY DIFFRACTION	100
2.2391-2.3113	0.1878	135	0.1363	6417	X-RAY DIFFRACTION	100
2.3113-2.3939	0.1525	136	0.1301	6339	X-RAY DIFFRACTION	100
2.3939-2.4897	0.1789	142	0.1319	6386	X-RAY DIFFRACTION	100
2.4897-2.603	0.1742	138	0.1334	6325	X-RAY DIFFRACTION	100
2.603-2.7401	0.1721	136	0.1304	6408	X-RAY DIFFRACTION	100
2.7401-2.9117	0.1828	138	0.1324	6376	X-RAY DIFFRACTION	100
2.9117-3.1363	0.1784	138	0.1342	6364	X-RAY DIFFRACTION	100
3.1363-3.4516	0.201	139	0.1235	6387	X-RAY DIFFRACTION	100
3.4516-3.9503	0.1792	140	0.1134	6348	X-RAY DIFFRACTION	100
3.9503-4.9739	0.1247	137	0.1117	6377	X-RAY DIFFRACTION	100
4.9739-31.8114	0.1975	131	0.1624	6351	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	2.1383	0.0316	0.3199	1.0321	-0.1999	1.2303	-0.0644	0.2278	0.2011	-0.1538	0.0346	-0.0843	0.0335	0.0003	0.0422	0.1601	-0.0223	0.0237	0.136	0.036	0.168	15.7084	24.0054	4.6584
2	1.5665	-0.1195	0.6175	1.3853	-0.8098	2.146	-0.0885	0.0725	0.0389	-0.0613	0.1012	0.0099	-0.0151	-0.1282	-0.0254	0.1377	-0.0196	0.0151	0.1327	-0.0025	0.1569	6.8168	14.1553	10.5444
3	5.3788	1.5618	1.1304	6.0216	-2.5205	5.3546	0.0814	-0.8156	0.3618	0.6207	0.0206	-0.146	-0.3668	0.0778	-0.1275	0.1951	0.01	-0.0275	0.241	-0.0735	0.1915	22.6627	22.846	29.2848
4	1.2457	0.1103	0.2822	1.2526	0.1396	1.6488	-0.0558	0.0852	0.1769	-0.1228	0.0346	-0.135	-0.117	0.0167	0.0099	0.1217	-0.0219	0.0259	0.1197	0.0212	0.1905	18.2739	25.5474	8.5655
5	7.4073	-4.4659	2.7919	3.15	-0.9757	2.336	0.0848	0.5352	0.0636	-0.6342	0.1772	0.5815	-0.2437	-0.4255	-0.1911	0.405	-0.0639	0.0157	0.3477	0.1141	0.3394	12.672	29.1127	-7.8752
6	2.6015	-0.278	0.7693	0.8873	-0.0772	1.3247	-0.0667	-0.1447	0.2872	0.1182	0.0432	-0.0533	-0.0362	0.053	0.0407	0.1596	0.0326	0.0093	0.1278	-0.0259	0.1544	-16.4792	23.3937	28.1408
7	1.2615	-0.1848	0.4311	0.7716	-0.0506	1.5079	-0.0411	-0.0356	-0.0544	0.0324	0.0645	-0.0083	0.0322	0.0279	-0.031	0.1536	0.0101	0.0157	0.1491	0.0042	0.1562	-10.2892	12.459	20.1822
8	3.8704	-1.3288	1.281	7.0437	4.9519	4.8341	0.0899	1.166	0.5248	-1.1298	-0.0277	-0.5662	-0.4361	0.4284	-0.0287	0.2581	-0.0088	-0.012	0.4988	0.1646	0.3926	-27.6615	22.7643	2.2339
9	1.2485	-0.0716	0.2332	1.0856	-0.1398	1.7529	-0.0342	-0.0786	0.178	0.0926	0.0569	0.0922	-0.129	-0.0355	-0.0229	0.1133	0.024	0.0259	0.122	-0.0104	0.1536	-20.7881	23.0032	24.8851
10	6.9055	4.7616	2.2267	7.7018	1.7485	9.0215	-0.0613	-0.8479	0.1807	0.6131	0.1914	-0.6919	0.1744	0.1267	-0.0627	0.2918	0.1122	-0.0196	0.3187	-0.1082	0.3007	-15.8671	27.0287	41.3167

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 244:325)
2	X-RAY DIFFRACTION	2	(chain A and resid 326:426)
3	X-RAY DIFFRACTION	3	(chain A and resid 427:457)
4	X-RAY DIFFRACTION	4	(chain A and resid 458:566)
5	X-RAY DIFFRACTION	5	(chain A and resid 567:578)
6	X-RAY DIFFRACTION	6	(chain B and resid 244:334)
7	X-RAY DIFFRACTION	7	(chain B and resid 335:439)
8	X-RAY DIFFRACTION	8	(chain B and resid 440:458)
9	X-RAY DIFFRACTION	9	(chain B and resid 459:566)
10	X-RAY DIFFRACTION	10	(chain B and resid 567:578)

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 1081 molecules

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 1081 molecules

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 1081 molecules

-
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