PDB-4xwt: Crystal structure of RNase J complexed with UMP

ID or keywords:

Entry

Database: PDB / ID: 4xwt

Title

Crystal structure of RNase J complexed with UMP

Components

DR2417

Keywords

RNA BINDING PROTEIN /

ribonuclease / two-metal-ion /

dimerization /

manganese /

Deinococcus radiodurans

Function / homology

Function and homology information

5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing /

Hydrolases; Acting on ester bonds /

RNA binding / zinc ion binding /

cytoplasm
Similarity search - Function

Biological species

Deinococcus radiodurans (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.003 Å

Authors

Lu, M. / Zhang, H. / Xu, Q. / Hua, Y. / Zhao, Y.

Funding support

China, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J
Authors: Zhao, Y. / Lu, M. / Zhang, H. / Hu, J. / Zhou, C. / Xu, Q. / Shah, A.M.U.H. / Xu, H. / Wang, L. / Hua, Y.

History

Deposition	Jan 29, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4xwt.cif.gz	430.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4xwt.ent.gz	365.6 KB	Display	PDB format
PDBx/mmJSON format	4xwt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4xwt_validation.pdf.gz	996.6 KB	Display	wwPDB validaton report
Full document	4xwt_full_validation.pdf.gz	1021.6 KB	Display
Data in XML	4xwt_validation.xml.gz	44.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xw/4xwt ftp://data.pdbj.org/pub/pdb/validation_reports/xw/4xwt	HTTPS FTP

-
Related structure data

Related structure data	4xwwC C: citing same article (ref.)
Similar structure data	4xww-d 1pn0-1 4f7z-d 3t3o-1 4c75-d 7812 2cm3-1 2po4-d 5b47-d 1qf6-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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #254 - Feb 2021 Cellulose Synthase similarity (1) #86 - Feb 2007 Exosomes similarity (1) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: DR2417

B: DR2417

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.590, 87.760, 253.420
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

biological unit is the same as asym.

-
Protein , 1 types, 2 molecules AB

#1: Protein	DR2417 Mass: 61701.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rossetta / References: UniProt: H9CZL7

-
Non-polymers , 5 types, 332 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₃N₂O₉P
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 322 / 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: 3 Å³/Da / Density % sol: 59 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000, MnCl2, MES

-
Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2→30 Å / Num. obs: 98253 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 6 % / B_iso Wilson estimate: 33.99 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.065 / R_rim(I) all: 0.072 / Χ²: 1.042 / Net I/σ(I): 16.09 / Num. measured all: 588280

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2-2.06		0.831	0.657	3.25	42663	7315	7177	0.716	98.1
2.06-2.11		0.896	0.493	4.24	44143	7225	7209	0.537	99.8
2.11-2.17		0.929	0.411	5.11	42482	6958	6946	0.447	99.8
2.17-2.24		0.959	0.323	6.21	41590	6805	6786	0.352	99.7
2.24-2.31		0.966	0.265	7.44	40236	6601	6582	0.289	99.7
2.31-2.39		0.978	0.217	8.74	39149	6376	6360	0.237	99.7
2.39-2.48		0.985	0.172	10.68	37527	6147	6123	0.188	99.6
2.48-2.59		0.989	0.141	12.68	36003	5945	5910	0.154	99.4
2.59-2.7		0.991	0.116	14.78	34363	5703	5666	0.126	99.4
2.7-2.83		0.994	0.094	17.56	32601	5468	5404	0.103	98.8
2.83-2.99		0.996	0.075	21.02	30553	5192	5113	0.083	98.5
2.99-3.17		0.996	0.062	24.74	28396	4939	4821	0.068	97.6
3.17-3.39		0.997	0.052	28.32	26334	4644	4504	0.057	97
3.39-3.66		0.997	0.047	30.78	24042	4331	4193	0.052	96.8
3.66-4.01		0.998	0.041	33.25	21752	4016	3857	0.045	96
4.01-4.48		0.998	0.038	35.84	20639	3647	3479	0.041	95.4
4.48-5.17		0.998	0.034	36.31	17806	3249	3059	0.038	94.2
5.17-6.33		0.998	0.033	36.29	15211	2757	2597	0.037	94.2
6.33-8.96		0.998	0.034	35.4	10204	2186	1865	0.037	85.3
	8.96	0.997	0.037	31.16	2586	1291	602	0.041	46.6

-
Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XSCALE		data reduction
PDB_EXTRACT	3.15	data extraction
Coot		model building
XDS		data processing

Refinement

Resolution: 2.003→29.473 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2352	4898	4.99 %
R_work	0.2002	-	-
obs	0.2019	98248	97.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.003→29.473 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8288	0	60	322	8670

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8587
X-RAY DIFFRACTION	f_angle_d	1.121	11698
X-RAY DIFFRACTION	f_dihedral_angle_d	16.23	3168
X-RAY DIFFRACTION	f_chiral_restr	0.044	1339
X-RAY DIFFRACTION	f_plane_restr	0.005	1546

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 (%)
2.0034-2.0261	0.3176	148	0.2832	3038	X-RAY DIFFRACTION	97
2.0261-2.05	0.327	163	0.2776	3128	X-RAY DIFFRACTION	99
2.05-2.0749	0.3154	164	0.2662	3185	X-RAY DIFFRACTION	100
2.0749-2.1012	0.2804	169	0.2546	3099	X-RAY DIFFRACTION	100
2.1012-2.1288	0.3015	151	0.2568	3168	X-RAY DIFFRACTION	100
2.1288-2.158	0.3221	154	0.2577	3190	X-RAY DIFFRACTION	100
2.158-2.1888	0.2674	152	0.2528	3132	X-RAY DIFFRACTION	100
2.1888-2.2215	0.2945	168	0.2471	3155	X-RAY DIFFRACTION	99
2.2215-2.2562	0.2867	144	0.2377	3149	X-RAY DIFFRACTION	100
2.2562-2.2932	0.2732	165	0.2452	3171	X-RAY DIFFRACTION	100
2.2932-2.3327	0.3162	163	0.2365	3098	X-RAY DIFFRACTION	100
2.3327-2.3751	0.2848	187	0.2359	3214	X-RAY DIFFRACTION	100
2.3751-2.4207	0.2552	163	0.2301	3100	X-RAY DIFFRACTION	100
2.4207-2.4701	0.2998	163	0.23	3174	X-RAY DIFFRACTION	99
2.4701-2.5238	0.2837	152	0.2244	3145	X-RAY DIFFRACTION	100
2.5238-2.5825	0.2819	158	0.2231	3182	X-RAY DIFFRACTION	99
2.5825-2.647	0.2564	165	0.2294	3152	X-RAY DIFFRACTION	100
2.647-2.7186	0.2708	170	0.2188	3136	X-RAY DIFFRACTION	99
2.7186-2.7985	0.2727	179	0.2224	3121	X-RAY DIFFRACTION	98
2.7985-2.8887	0.2834	169	0.2298	3154	X-RAY DIFFRACTION	99
2.8887-2.9919	0.2391	170	0.2071	3124	X-RAY DIFFRACTION	99
2.9919-3.1116	0.2594	166	0.2146	3117	X-RAY DIFFRACTION	98
3.1116-3.253	0.2711	164	0.1981	3140	X-RAY DIFFRACTION	98
3.253-3.4243	0.2299	162	0.19	3086	X-RAY DIFFRACTION	97
3.4243-3.6385	0.2293	156	0.1875	3127	X-RAY DIFFRACTION	97
3.6385-3.9188	0.1836	166	0.1642	3087	X-RAY DIFFRACTION	96
3.9188-4.3121	0.166	185	0.1552	3080	X-RAY DIFFRACTION	96
4.3121-4.9335	0.1796	180	0.1474	3069	X-RAY DIFFRACTION	94
4.9335-6.2061	0.1958	155	0.1709	3113	X-RAY DIFFRACTION	94
6.2061-29.4761	0.2342	147	0.2136	2516	X-RAY DIFFRACTION	73

Refinement TLS params.

Method: refined / Origin x: 1.4293 Å / Origin y: 181.8578 Å / Origin z: 27.3601 Å

	11	12	13	21	22	23	31	32	33
T	0.3566 Å²	-0.1454 Å²	-0.0012 Å²	-	0.3402 Å²	-0.0391 Å²	-	-	0.2203 Å²
L	0.756 °²	-0.2834 °²	0.1361 °²	-	1.9878 °²	-0.0174 °²	-	-	0.4992 °²
S	0.0401 Å °	-0.0863 Å °	-0.0855 Å °	0.4065 Å °	-0.0088 Å °	0.0553 Å °	0.0327 Å °	-0.0137 Å °	-0.026 Å °

Refinement TLS group

Selection details: all

-
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, 332 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, 332 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, 332 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