PDB-4rl9: Crystal structure of Acinetobacter baumannii CarO1

ID or keywords:

Entry

Database: PDB / ID: 4rl9

Title

Crystal structure of Acinetobacter baumannii CarO1

Components

Carbapenem-associated resistance protein

Keywords

MEMBRANE PROTEIN / outer membrane protein / beta-barrel

Function / homology

Porin - #170 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta / CarO

Function and homology information

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Zahn, M. / Basle, A. / van den Berg, B.

Citation

Journal: J.Mol.Biol. / Year: 2015
Title: Small-Molecule Transport by CarO, an Abundant Eight-Stranded beta-Barrel Outer Membrane Protein from Acinetobacter baumannii.
Authors: Zahn, M. / D'Agostino, T. / Eren, E. / Basle, A. / Ceccarelli, M. / van den Berg, B.

History

Deposition	Oct 16, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4rl9.cif.gz	169.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4rl9.ent.gz	135.6 KB	Display	PDB format
PDBx/mmJSON format	4rl9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4rl9_validation.pdf.gz	443.1 KB	Display	wwPDB validaton report
Full document	4rl9_full_validation.pdf.gz	449 KB	Display
Data in XML	4rl9_validation.xml.gz	15.7 KB	Display
Data in CIF	4rl9_validation.cif.gz	20.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rl/4rl9 ftp://data.pdbj.org/pub/pdb/validation_reports/rl/4rl9	HTTPS FTP

-
Related structure data

Related structure data	4rlbC 4rlcC 4fuv C: citing same article (ref.)
Similar structure data	4rlb-2 3zy7-d 5nlz-d 1cdy-d 1bhh-d 2xgl-d 5w7j-2 5j6e-d 4wt3-d 6d9i-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 - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: Carbapenem-associated resistance protein

B: Carbapenem-associated resistance protein

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

1

A: Carbapenem-associated resistance protein

defined by author
28.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Carbapenem-associated resistance protein

defined by author
28.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	145.774, 63.260, 73.668
Angle α, β, γ (deg.)	90.00, 119.70, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 17 - 227 / Label seq-ID: 44 - 254

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	Carbapenem-associated resistance protein Mass: 28070.834 Da / Num. of mol.: 2 / Fragment: UNP residues 22-249 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: carO / Production host: Escherichia coli (E. coli) / References: UniProt: A6XB80

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.19 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 9% PEG8000, 0.04 M zinc acetate, 0.05 M ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2014
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.7→63.99 Å / Num. obs: 16167 / % possible obs: 99.7 %
Reflection shell	Resolution: 2.7→2.83 Å / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
GDA		data collection
MOLREP		phasing
REFMAC	5.8.0073	refinement
XDS		data reduction
XDS	/ XSCALE	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→63.99 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.884 / SU B: 28.615 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.673 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27806	778	4.8 %	RANDOM
R_work	0.23258	-	-	-
obs	0.23497	15388	99.61 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 71.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.57 Å²	-0 Å²	0.69 Å²
2-	-	2.02 Å²	-0 Å²
3-	-	-	-0.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→63.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3139	0	0	0	3139

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.02	3220
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	2904
X-RAY DIFFRACTION	r_angle_refined_deg	1.586	1.939	4388
X-RAY DIFFRACTION	r_angle_other_deg	0.965	3	6663
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.406	5	405
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.452	25.472	159
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.586	15	463
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.898	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	445
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	3834
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	768
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.677	5.23	1632
X-RAY DIFFRACTION	r_mcbond_other	3.677	5.229	1631
X-RAY DIFFRACTION	r_mcangle_it	5.52	7.837	2033
X-RAY DIFFRACTION	r_mcangle_other	5.519	7.837	2034
X-RAY DIFFRACTION	r_scbond_it	4.39	5.832	1588
X-RAY DIFFRACTION	r_scbond_other	4.389	5.831	1589
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.912	8.575	2356
X-RAY DIFFRACTION	r_long_range_B_refined	9.4	44.027	3472
X-RAY DIFFRACTION	r_long_range_B_other	9.399	44.031	3473
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 10320 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	51	-
R_work	0.315	1159	-
obs	-	-	99.02 %

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	2.1726	1.749	-2.1102	3.4083	-2.7488	2.8976	-0.0821	-0.1852	0.0642	0.1835	0.047	0.0525	-0.1639	0.0609	0.0351	0.1363	0.0312	0.0201	0.0367	-0.0193	0.1721	15.6574	3.8529	31.7956
2	6.6787	-0.8507	-4.0464	0.154	0.6391	3.0755	0.1133	-0.179	-0.0226	0.0256	0.0233	-0.0087	-0.0173	0.2488	-0.1366	0.114	0.0045	-0.0229	0.1114	-0.0385	0.136	28.2882	8.7156	14.2729
3	0.7185	0.0141	-0.6257	0.684	-0.7406	1.3416	0.0031	0.0432	-0.0922	0.0294	-0.0022	0.0516	0.0081	-0.0283	-0.0009	0.1119	-0.0133	0.0138	0.0219	-0.0604	0.1769	22.9385	-2.2845	20.6294
4	1.6046	-0.4147	-0.6444	0.177	-0.1567	1.8032	0.0267	0.2912	-0.0928	0.0001	-0.06	0.0236	0.0312	-0.1934	0.0334	0.1224	0.0046	-0.015	0.0581	-0.0325	0.1729	25.0806	0.8571	10.3053
5	0.3981	-0.2319	0.7931	0.6714	1.1425	6.6717	0.0141	0.025	-0.0461	0.0297	-0.0589	0.0155	0.2194	-0.0716	0.0448	0.0896	-0.0239	0.0246	0.0356	-0.0196	0.1528	19.4009	-2.3106	17.4787
6	0.5697	-0.4322	1.3616	0.6041	-0.6079	4.2527	-0.0193	0.0323	0.043	0.0914	0.0466	-0.1176	0.0798	-0.1097	-0.0273	0.0333	0.0116	0.007	0.2747	-0.0201	0.1214	40.0711	-15.7079	32.0427
7	1.4341	0.8286	-0.245	0.5036	-0.3141	2.168	0.1116	0.4516	-0.0873	0.0282	0.1734	-0.0333	0.4318	0.2227	-0.285	0.119	0.142	-0.033	0.3868	-0.0595	0.352	48.953	-12.8762	45.9306
8	1.9931	0.9656	0.3413	0.5081	-0.0042	1.0363	0.2281	0.0552	0.1388	0.0841	-0.0387	0.1042	0.1426	0.119	-0.1894	0.0675	0.0667	-0.0036	0.1552	-0.0122	0.2174	51.6546	-7.5459	56.4585
9	1.8703	-0.0045	-0.004	0.6495	0.5908	0.5467	0.0844	0.6172	0.2973	0.0066	0.1011	-0.1609	-0.0006	0.0824	-0.1855	0.0228	-0.0049	0.068	0.3283	0.0347	0.3225	42.3089	-8.9879	40.7058
10	2.3381	0.8775	0.8515	0.4136	0.2753	0.6725	-0.0136	-0.0703	0.2377	0.0433	-0.0627	0.2214	-0.0688	0.1331	0.0763	0.0344	-0.033	0.0634	0.077	-0.036	0.2589	47.2215	-3.0719	56.9339

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	18 - 54
2	X-RAY DIFFRACTION	2	A	55 - 75
3	X-RAY DIFFRACTION	3	A	76 - 126
4	X-RAY DIFFRACTION	4	A	127 - 203
5	X-RAY DIFFRACTION	5	A	204 - 228
6	X-RAY DIFFRACTION	6	B	17 - 54
7	X-RAY DIFFRACTION	7	B	55 - 84
8	X-RAY DIFFRACTION	8	B	92 - 138
9	X-RAY DIFFRACTION	9	B	139 - 181
10	X-RAY DIFFRACTION	10	B	182 - 227

-
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://pdbjlvh1.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