PDB-5tw9: 1.50 Angstrom Crystal Structure of C-terminal Fragment (residues ...

ID or keywords:

Entry

Database: PDB / ID: 5tw9

Title

1.50 Angstrom Crystal Structure of C-terminal Fragment (residues 322-384) of Iron Uptake System Component EfeO from Yersinia pestis.

Components

Iron uptake system component EfeO

Keywords

LIPID BINDING PROTEIN /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / iron uptake system component EfeO / Lipid-Binding Protein

Function / homology

Function and homology information

periplasmic space
Similarity search - Function

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.5 Å

Authors

Minasov, G. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.50 Angstrom Crystal Structure of C-terminal Fragment (residues 322-384) of Iron Uptake System Component EfeO from Yersinia pestis.
Authors: Minasov, G. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Nov 11, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 30, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / struct_keywords Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.pdbx_keywords

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5tw9.cif.gz	177.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5tw9.ent.gz	145.5 KB	Display	PDB format
PDBx/mmJSON format	5tw9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/5tw9 ftp://data.pdbj.org/pub/pdb/validation_reports/tw/5tw9	HTTPS FTP

-
Related structure data

Similar structure data	3zqy-d 4i45-d 1lo7-d 5vde-2 2ggp-d 5vdf-1 1zuk-d 1lo9-d 1cmz-d 2ykz-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) 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: CSGID-IDP91016

Similar structure data

Other databases

TargetTrack: CSGID-IDP91016

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Iron uptake system component EfeO

B: Iron uptake system component EfeO

C: Iron uptake system component EfeO

D: Iron uptake system component EfeO

E: Iron uptake system component EfeO

F: Iron uptake system component EfeO

hetero molecules

44.4 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Iron uptake system component EfeO

B: Iron uptake system component EfeO

hetero molecules

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

2

C: Iron uptake system component EfeO

D: Iron uptake system component EfeO

hetero molecules

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

3

E: Iron uptake system component EfeO

F: Iron uptake system component EfeO

hetero molecules

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

Unit cell

Length a, b, c (Å)	34.037, 64.001, 173.151
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Iron uptake system component EfeO Mass: 6993.880 Da / Num. of mol.: 6 / Fragment: C-terminal Fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: efeO, YPO1855, y2451, YP_1538 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q0WFT9
#2: Chemical	ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.2 Å³/Da / Density % sol: 44.6 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein: 14.1 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (E3), 0.2M Sodium iodide, 20% (w/v) PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2016 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.5→30 Å / Num. obs: 62217 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / B_iso Wilson estimate: 18.8 Å² / R_merge(I) obs: 0.067 / R_sym value: 0.067 / Net I/σ(I): 43.4
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.66 / Mean I/σ(I) obs: 3.8 / CC_1/2: 0.933 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.5→29.61 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.955 / SU B: 2.657 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2025	3112	5 %	RANDOM
R_work	0.17293	-	-	-
obs	0.17442	58666	99.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 22.542 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.28 Å²	0 Å²	0 Å²
2-	-	0.73 Å²	0 Å²
3-	-	-	-1.02 Å²

Refinement step

Cycle: 1 / Resolution: 1.5→29.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2928	0	33	409	3370

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	3285
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3223
X-RAY DIFFRACTION	r_angle_refined_deg	1.278	2.003	4456
X-RAY DIFFRACTION	r_angle_other_deg	0.813	3	7457
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.834	5	429
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.312	25.287	157
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.654	15	624
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.435	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	495
X-RAY DIFFRACTION	r_gen_planes_refined	0.025	0.02	3851
X-RAY DIFFRACTION	r_gen_planes_other	0.021	0.02	693
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	0.927	1.366	1650
X-RAY DIFFRACTION	r_mcbond_other	0.921	1.364	1649
X-RAY DIFFRACTION	r_mcangle_it	1.6	2.026	2101
X-RAY DIFFRACTION	r_mcangle_other	1.601	2.028	2102
X-RAY DIFFRACTION	r_scbond_it	1.171	1.546	1635
X-RAY DIFFRACTION	r_scbond_other	1.171	1.546	1635
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.872	2.256	2356
X-RAY DIFFRACTION	r_long_range_B_refined	4.772	21.459	4003
X-RAY DIFFRACTION	r_long_range_B_other	4.573	20.764	3900
X-RAY DIFFRACTION	r_rigid_bond_restr	12.991	3	2
X-RAY DIFFRACTION	r_sphericity_free	19.019	5	9
X-RAY DIFFRACTION	r_sphericity_bonded	19.256	5	13

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.214	237	-
R_work	0.207	4266	-
obs	-	-	99.96 %

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	1.1683	1.3435	2.2476	2.1915	2.9464	6.428	-0.0079	0.0026	0.0151	-0.0401	-0.0411	0.1212	-0.2493	-0.0382	0.049	0.0365	0.0107	0.0107	0.0074	0.0005	0.0305	3.058	37.2393	80.9764
2	3.4066	1.5327	-0.2627	6.8094	-2.0463	4.6079	-0.0318	0.124	0.054	-0.067	0.1202	0.3337	0.3101	-0.2706	-0.0884	0.0321	-0.0099	-0.0154	0.0327	-0.0179	0.0581	-3.8053	22.4637	71.3545
3	0.6214	0.3505	1.1217	0.4236	1.2895	9.313	0.0502	0.0213	-0.0392	0.0344	-0.0146	-0.0247	0.0533	0.3178	-0.0356	0.0223	0.0037	0.0077	0.0298	0.0046	0.0343	10.4814	33.4636	82.7785
4	1.322	0.0298	-0.5317	3.8329	4.8952	8.2151	0.0172	0.0172	-0.0455	0.0751	-0.1081	0.0901	0.0672	-0.268	0.0909	0.0234	0.0008	0.0188	0.012	0.0009	0.0184	-1.4669	28.6213	88.5641
5	3.4244	-2.4472	1.8275	3.6265	-1.6471	1.0866	-0.065	0.0421	0.1798	0.3399	-0.0353	0.1043	-0.191	-0.0139	0.1002	0.3116	0.0181	0.0102	0.1418	-0.0205	0.172	0.8848	44.9998	99.406
6	0.5324	-0.3931	-2.0611	1.1298	2.2367	8.9408	0.0039	-0.1078	-0.0114	0.0304	0.042	-0.0265	0.0812	0.4256	-0.0459	0.0276	0.0062	-0.0005	0.0282	-0.0023	0.024	6.6306	27.7882	90.8861
7	1.0834	-0.8348	-1.7577	2.7562	3.0632	7.5002	-0.0207	-0.0124	-0.0459	0.0926	-0.0427	0.0667	-0.1935	-0.1524	0.0634	0.0341	0.0119	-0.0069	0.0848	0.0133	0.0338	-4.6374	42.5276	53.6729
8	5.5945	-1.5127	1.9738	2.7892	-0.554	3.1317	0.1792	0.262	-0.4811	-0.0696	-0.1106	-0.1977	0.2336	0.3992	-0.0686	0.0229	0.0092	-0.0033	0.1383	-0.0106	0.1032	5.4107	33.6861	39.5236
9	0.1188	-0.2598	-0.4538	1.3242	2.5275	11.4093	-0.0597	0.0114	0.0105	0.034	0.0848	-0.0536	-0.3911	0.2883	-0.0252	0.0739	-0.0234	-0.0222	0.0609	0.0013	0.0438	1.7232	49.2953	55.105
10	2.5846	-0.9745	-0.892	6.3655	-0.7077	11.4114	-0.2362	0.0941	-0.3584	-0.1508	0.0083	-0.4387	0.466	0.321	0.2279	0.0427	0.0086	0.0544	0.1067	-0.0134	0.1226	7.7995	33.9265	53.5336
11	1.7842	-0.8975	0.3366	0.8735	0.8244	4.3907	-0.1385	0.0571	0.0431	-0.0293	-0.043	0.0643	-0.5032	-0.2198	0.1816	0.0967	0.0514	-0.0121	0.0464	0.0066	0.0473	-2.1727	42.4544	70.349
12	2.3268	0.056	-0.4904	1.1783	-0.2033	11.165	-0.0051	0.0914	0.0367	0.149	0.0069	-0.0165	-0.3068	0.1987	-0.0018	0.0286	-0.0164	-0.0062	0.0647	0.007	0.0308	8.689	44.5924	51.7021
13	1.4069	-0.2951	-1.1903	2.4164	3.5709	6.9587	0.0189	0.0693	0.0238	0.0209	-0.1031	0.0783	-0.0891	-0.1846	0.0842	0.0195	0.0162	-0.0049	0.0379	-0.0035	0.0316	4.5612	10.2521	56.0078
14	8.5973	-1.6125	1.6813	3.5833	0.0465	3.7373	0.2323	0.4493	-0.5139	-0.0405	-0.2178	-0.1354	0.4318	0.3406	-0.0145	0.0552	0.0556	0.0012	0.1284	-0.0377	0.0826	15.3332	-1.1389	43.0867
15	0.5789	-0.1935	-0.1125	0.6314	2.1279	8.1166	-0.0591	0.112	0.1463	-0.0269	0.0612	-0.0598	-0.2678	0.2239	-0.0021	0.0512	0.0038	-0.0191	0.0742	0.0003	0.0623	11.0575	15.5814	54.3565
16	4.8675	-0.0223	-3.007	5.1835	-0.8672	11.2199	-0.1756	0.1553	-0.2615	-0.0372	0.0046	-0.2102	0.3812	0.2754	0.171	0.0221	0.0152	0.0021	0.0352	-0.0147	0.0458	16.6584	1.2362	55.8568
17	2.1224	-0.8388	0.0689	1.4599	0.2684	1.1064	-0.097	-0.1079	-0.0019	0.1453	0.0747	0.0985	0.0043	-0.0975	0.0222	0.0678	0.0268	-0.0069	0.0329	0.0041	0.0269	7.5695	9.8929	72.4386
18	3.8928	-0.0889	0.3778	2.5869	-0.9297	11.3992	0.0158	0.2738	0.1874	0.1156	-0.094	-0.0582	-0.3233	0.0972	0.0783	0.014	0.0019	-0.0021	0.0458	0.0182	0.0459	17.9567	12.1036	52.6349

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	322 - 343
2	X-RAY DIFFRACTION	2	A	344 - 354
3	X-RAY DIFFRACTION	3	A	355 - 384
4	X-RAY DIFFRACTION	4	B	322 - 340
5	X-RAY DIFFRACTION	5	B	341 - 355
6	X-RAY DIFFRACTION	6	B	356 - 383
7	X-RAY DIFFRACTION	7	C	322 - 341
8	X-RAY DIFFRACTION	8	C	342 - 359
9	X-RAY DIFFRACTION	9	C	360 - 384
10	X-RAY DIFFRACTION	10	D	322 - 330
11	X-RAY DIFFRACTION	11	D	331 - 366
12	X-RAY DIFFRACTION	12	D	367 - 384
13	X-RAY DIFFRACTION	13	E	322 - 341
14	X-RAY DIFFRACTION	14	E	342 - 354
15	X-RAY DIFFRACTION	15	E	355 - 383
16	X-RAY DIFFRACTION	16	F	322 - 330
17	X-RAY DIFFRACTION	17	F	331 - 369
18	X-RAY DIFFRACTION	18	F	370 - 384

-
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