PDB-5i0m: Crystal structure of DR2231_E79A mutant in complex with dUMP

ID or keywords:

Entry

Database: PDB / ID: 5i0m

Title

Crystal structure of DR2231_E79A mutant in complex with dUMP

Components

DR2231

Keywords

HYDROLASE / alpha helix

Function / homology

Function and homology information

nucleoside triphosphate diphosphatase activity / metal ion binding
Similarity search - Function

Biological species

Deinococcus radiodurans (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Mota, C.S. / Goncalves, A.M.D. / de Sanctis, D.

Funding support

Portugal, 1items

Citation

Journal: FEBS J. / Year: 2016
Title: Deinococcus radiodurans DR2231 is a two-metal-ion mechanism hydrolase with exclusive activity on dUTP.
Authors: Mota, C.S. / Goncalves, A.M. / de Sanctis, D.

History

Deposition	Feb 4, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 14, 2016	Group: Database references
Revision 1.2	Apr 4, 2018	Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5i0m.cif.gz	213.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5i0m.ent.gz	172.2 KB	Display	PDB format
PDBx/mmJSON format	5i0m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5i0m_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5i0m_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5i0m_validation.xml.gz	26.5 KB	Display
Data in CIF	5i0m_validation.cif.gz	39.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i0/5i0m ftp://data.pdbj.org/pub/pdb/validation_reports/i0/5i0m	HTTPS FTP

-
Related structure data

Related structure data	5hvaC 5hwuC 5hx1C 5hylC 5hzzC 5i0jC 2yfcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4o8m-8 3p09-1 6s4u-2 2zlc-d 5xpl-d 6zyv-2 1ot7-1 5b5b-2 3hc6-d 4p32-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DR2231

B: DR2231

C: DR2231

D: DR2231

hetero molecules

60.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DR2231

D: DR2231

hetero molecules

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

2

B: DR2231

C: DR2231

hetero molecules

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

Unit cell

Length a, b, c (Å)	148.960, 78.267, 52.368
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	DR2231 Mass: 14974.816 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: DR_2231 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9RS96
#2: Chemical	ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₃N₂O₈P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.55 Å³/Da / Density % sol: 51.73 % / Mosaicity: 0.11 °
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 7.5 / Details: Lithium Acetate, PEG3350

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.939 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.939 Å / Relative weight: 1

Reflection

Resolution: 2.15→42.839 Å / Num. all: 34099 / Num. obs: 34099 / % possible obs: 99.8 % / Redundancy: 4 % / B_iso Wilson estimate: 20.22 Å² / R_pim(I) all: 0.094 / R_rim(I) all: 0.201 / R_sym value: 0.177 / Net I/av σ(I): 3.732 / Net I/σ(I): 10.3 / Num. measured all: 137850

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.15-2.27	4.1	0.802	0.9	1	99.9
2.27-2.4	4.1	0.59	1.1	1	99.9
2.4-2.57	4.1	0.495	1.4	1	99.9
2.57-2.78	4.1	0.355	1.8	1	99.9
2.78-3.04	4.1	0.224	2.9	1	99.8
3.04-3.4	4	0.143	4.4	1	99.8
3.4-3.93	4	0.084	7.8	1	99.8
3.93-4.81	3.9	0.057	11.6	1	99.7
4.81-6.8	3.8	0.057	11.6	1	99.8
6.8-42.839	3.7	0.028	19.7	1	98.6

-
Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX		refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdbid 2YFC

2yfc

Resolution: 2.15→42.839 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.62 / Phase error: 23.54

	R_factor	Num. reflection	% reflection
R_free	0.2342	3272	5.11 %
R_work	0.184	-	-
obs	0.1866	34035	99.42 %

Solvent computation

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

Displacement parameters

B_iso max: 82.86 Å² / B_iso mean: 23.8036 Å² / B_iso min: 4.54 Å²

Refinement step

Cycle: final / Resolution: 2.15→42.839 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3904	0	40	553	4497
B_iso mean	-	-	14.95	32.57	-
Num. residues	-	-	-	-	510

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4026
X-RAY DIFFRACTION	f_angle_d	0.805	5486
X-RAY DIFFRACTION	f_chiral_restr	0.04	620
X-RAY DIFFRACTION	f_plane_restr	0.006	736
X-RAY DIFFRACTION	f_dihedral_angle_d	20.356	1502

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.15-2.1821	0.3454	155	0.2709	2671	2826	100
2.1821-2.2162	0.3614	132	0.2597	2633	2765	100
2.2162-2.2525	0.3034	127	0.2448	2672	2799	100
2.2525-2.2914	0.2912	162	0.2325	2666	2828	100
2.2914-2.333	0.278	143	0.215	2585	2728	100
2.333-2.3779	0.2614	156	0.1979	2688	2844	100
2.3779-2.4264	0.2394	161	0.2044	2580	2741	100
2.4264-2.4792	0.2429	138	0.1996	2690	2828	100
2.4792-2.5368	0.2944	131	0.2007	2608	2739	100
2.5368-2.6003	0.2651	163	0.1978	2635	2798	100
2.6003-2.6706	0.2326	144	0.2014	2651	2795	100
2.6706-2.7491	0.2953	123	0.1979	2663	2786	100
2.7491-2.8379	0.2629	109	0.1792	2652	2761	100
2.8379-2.9393	0.2013	129	0.1757	2665	2794	99
2.9393-3.0569	0.2089	129	0.1633	2646	2775	99
3.0569-3.196	0.242	171	0.1606	2610	2781	100
3.196-3.3644	0.2123	134	0.1583	2651	2785	99
3.3644-3.5751	0.2019	134	0.1568	2645	2779	99
3.5751-3.851	0.1763	149	0.1505	2619	2768	99
3.851-4.2383	0.2068	129	0.1506	2644	2773	99
4.2383-4.8508	0.1872	146	0.1541	2636	2782	99
4.8508-6.1087	0.24	145	0.1883	2608	2753	99
6.1087-42.8472	0.219	162	0.2071	2591	2753	98

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	0.0175	0.0116	0.005	0.006	0.0065	0.0012	0.0239	-0.0421	-0.0881	0.0983	-0.0205	-0.0843	-0.0573	0.0316	0	0.15	-0.0107	0.0041	0.1486	0.0149	0.147	-12.4022	-26.5683	-14.0031
2	0.0296	0.0026	0.0245	0.02	-0.0104	0.0197	-0.018	0.0046	0.1268	0.0444	-0.0291	0.0534	-0.053	0.0483	-0.0011	0.1417	-0.0199	-0.0252	0.0766	0.0106	0.1237	-25.4765	-11.0942	-26.5179
3	0.0402	-0.0115	0.0416	0.0705	0.0224	0.0594	-0.0762	-0.0085	0.0272	0.0232	0.1487	-0.0097	0.0582	0.0802	0.1786	0.0531	-0.1172	0.0057	-0.1514	0.0787	0.052	-22.4192	-25.5846	-23.7382
4	0.0033	-0.0341	0.0628	0.0697	-0.1142	0.1977	0.0913	0.0189	-0.1008	0.0584	-0.0178	0.0151	0.0421	-0.1536	0.039	0.1482	-0.096	-0.0492	0.0258	0.0234	0.1141	-34.6817	-34.3476	-21.8637
5	0.0051	-0.014	-0.0101	0.072	0.0608	0.056	-0.0022	0.0387	-0.0882	-0.0351	-0.0578	0.0278	-0.0233	-0.0673	-0.023	0.0863	-0.0529	-0.0166	0.2636	0.0093	0.1732	-69.0776	-27.9207	-7.5529
6	0.3265	0.1279	-0.158	0.0945	-0.0288	0.1421	0.0023	0.152	0.1137	0.0079	0.0822	-0.0153	-0.0348	-0.1614	0.0345	0.1558	0.0533	-0.0339	0.1135	0.0097	0.1205	-56.3154	-16.2548	-6.3788
7	0.0554	0.0625	-0.0541	0.0501	-0.0712	0.0714	-0.0232	-0.0484	-0.0363	-0.0042	0.0304	0.0542	0.0006	-0.1782	0.0001	0.0843	0.018	-0.0146	0.1159	-0.0049	0.1079	-56.4313	-25.0084	0.0125
8	0.0334	0.0212	-0.0165	0.0114	-0.0105	0.0214	0.0914	0.0115	-0.1406	-0.0415	-0.0494	-0.0488	0.0978	0.0681	-0.0002	0.0858	0.0128	-0.0191	0.0752	-0.0068	0.1029	-38.3059	-32.305	2.3916
9	0.0052	0.0104	0.0088	0.0404	0.0172	0.0122	-0.0308	0.0493	-0.0414	0.0153	0.0063	-0.0117	0.0259	-0.0222	-0.022	0.2439	-0.0355	-0.0488	0.0987	-0.0889	0.0907	-53.3082	-38.9872	-16.6082
10	0.012	-0.0156	0.0119	0.0247	-0.0046	0.0122	-0.0147	-0.1482	-0.0011	0.15	0.0088	0.0898	0.063	-0.0811	0.0005	0.0771	-0.0182	0.0003	0.1623	0.0087	0.1224	-54.0773	-30.7826	10.6968
11	0.1214	-0.0269	0.0978	0.0672	0.0102	0.0955	0.0233	-0.0003	0.0415	-0.0053	-0.017	-0.0303	-0.0673	-0.156	0.0033	0.0744	0.0021	-0.0053	0.1079	-0.0101	0.0753	-55.1391	-22.2366	-2.0525
12	0.1638	0.1088	0.001	0.0716	-0.0089	0.0359	-0.0539	0.1115	-0.1789	-0.1027	0.0735	-0.1229	0.0813	0.0446	-0.0116	0.1143	-0.0238	-0.0172	0.1126	-0.0176	0.1136	-24.6224	-29.6355	-36.9371
13	0.0833	-0.0189	0.0159	0.0764	0.04	0.0672	0.0431	-0.0419	0.0377	-0.0099	0.0004	0.0377	0.0137	-0.0356	0.0177	0.0618	-0.0228	-0.0082	0.0461	0.0006	0.075	-30.5853	-22.1058	-18.959
14	0.0395	-0.0175	-0.0271	0.0077	0.0214	0.0226	-0.066	0.1848	0.0138	0.0077	-0.0331	0.0032	-0.0165	0.0288	-0.0068	0.0678	-0.0185	-0.0144	0.1574	0.0375	0.1045	-11.6211	-19.2512	-33.8381

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 33 )	A	7 - 33
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 70 )	A	34 - 70
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 112 )	A	71 - 112
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 113 through 144 )	A	113 - 144
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 7 through 21 )	B	7 - 21
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 22 through 64 )	B	22 - 64
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 65 through 112 )	B	65 - 112
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 113 through 133 )	B	113 - 133
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 134 through 144 )	B	134 - 144
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 7 through 33 )	C	7 - 33
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 34 through 143 )	C	34 - 143
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 7 through 33 )	D	7 - 33
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 34 through 93 )	D	34 - 93
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 94 through 143 )	D	94 - 143

-
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