[English] 日本語

Yorodumi

- PDB-5opl: Crystal structure of K25E cN-II mutant -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 5opl

Title

Crystal structure of K25E cN-II mutant

Components

Cytosolic purine 5'-nucleotidase

Keywords

HYDROLASE / nucleotidase / relapsed leukemia

Function / homology

Function and homology information

nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Kugler, M. / Hnizda, A. / Pachl, P. / Rezacova, P.

Funding support

Czech Republic, 1items

Citation

Journal: Leukemia / Year: 2018
Title: Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation.
Authors: Hnizda, A. / Fabry, M. / Moriyama, T. / Pachl, P. / Kugler, M. / Brinsa, V. / Ascher, D.B. / Carroll, W.L. / Novak, P. / Zaliova, M. / Trka, J. / Rezacova, P. / Yang, J.J. / Veverka, V.

History

Deposition	Aug 10, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 13, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	5opl.cif.gz	221.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5opl.ent.gz	175.8 KB	Display	PDB format
PDBx/mmJSON format	5opl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5opl_validation.pdf.gz	439.3 KB	Display	wwPDB validaton report
Full document	5opl_full_validation.pdf.gz	442.5 KB	Display
Data in XML	5opl_validation.xml.gz	22.7 KB	Display
Data in CIF	5opl_validation.cif.gz	34 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/op/5opl ftp://data.pdbj.org/pub/pdb/validation_reports/op/5opl	HTTPS FTP

-
Related structure data

Related structure data	5opkC 5opmC 5opnC 5opoC 5oppC C: citing same article (ref.)
Similar structure data	5k7y-1 5opp-1 5opn-1 6dd3-1 5l50-1 4h4b-1 6de3-1 5opo-1 5opm-1 6fir-1 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

-
Assembly

Deposited unit

A: Cytosolic purine 5'-nucleotidase

hetero molecules

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

1

A: Cytosolic purine 5'-nucleotidase

hetero molecules

A: Cytosolic purine 5'-nucleotidase

hetero molecules

A: Cytosolic purine 5'-nucleotidase

hetero molecules

A: Cytosolic purine 5'-nucleotidase

hetero molecules

defined by author&software
Evidence: gel filtration
260 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.262, 127.576, 129.988
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-1003- HOH

-
Components

#1: Protein	Cytosolic purine 5'-nucleotidase / Cytosolic 5'-nucleotidase II Mass: 64088.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Production host: Escherichia coli (E. coli) / References: UniProt: P49902, 5'-nucleotidase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H₂O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.1 M MOPS/HEPES-Na pH 7.5; 0.02 M of each carboxylic acid ; 10% w/v PEG 8000, 20% v/v ethylene glycol G6 Morpheus condition

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 2, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.8→49.05 Å / Num. obs: 66924 / % possible obs: 94.2 % / Redundancy: 3.9 % / B_iso Wilson estimate: 30.2 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / R_rim(I) all: 0.063 / Net I/σ(I): 16
Reflection shell	Resolution: 1.8→1.91 Å / Redundancy: 1.46 % / R_merge(I) obs: 0.659 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 7678 / CC_1/2: 0.571 / R_rim(I) all: 0.916 / % possible all: 67.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XDS		data reduction
MOLREP		phasing
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→49.05 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.943 / SU B: 5.866 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2137	1674	2.5 %	RANDOM
R_work	0.18989	-	-	-
obs	0.19047	65251	94.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 32.702 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.64 Å²	0 Å²	-0 Å²
2-	-	-0.02 Å²	0 Å²
3-	-	-	-0.62 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→49.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3828	0	55	364	4247

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	4076
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3813
X-RAY DIFFRACTION	r_angle_refined_deg	1.529	1.964	5505
X-RAY DIFFRACTION	r_angle_other_deg	0.963	3	8792
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.993	5	491
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.76	23.249	197
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.876	15	697
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.137	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	586
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4563
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1001
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	0.738	1.564	1923
X-RAY DIFFRACTION	r_mcbond_other	0.732	1.564	1922
X-RAY DIFFRACTION	r_mcangle_it	1.242	2.341	2414
X-RAY DIFFRACTION	r_mcangle_other	1.242	2.341	2415
X-RAY DIFFRACTION	r_scbond_it	1.006	1.799	2152
X-RAY DIFFRACTION	r_scbond_other	0.998	1.799	2152
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.658	2.608	3086
X-RAY DIFFRACTION	r_long_range_B_refined	6.908	14.382	4963
X-RAY DIFFRACTION	r_long_range_B_other	6.907	14.392	4964
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.801→1.848 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.544	71	-
R_work	0.503	2752	-
obs	-	-	54.41 %

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	10.4833	4.4589	-4.3274	6.5972	0.0316	6.3126	0.2781	0.1724	0.5315	-0.0495	-0.0833	0.0434	-0.5372	-0.0373	-0.1948	0.1781	0.0203	-0.0182	0.22	0.0375	0.1505	0.33	35.863	-30.632
2	4.9486	0.2811	-4.9368	15.2383	4.6488	6.5252	0.1003	-0.1407	0.1243	0.1671	0.0508	-0.0795	-0.0857	0.1565	-0.1512	0.3835	0.0085	-0.002	0.3664	0.0402	0.386	15.295	46.964	-25.692
3	6.8237	-0.9396	-1.0891	0.8565	1.5733	3.3	0.1646	0.1761	0.6246	-0.2015	-0.0356	-0.1776	-0.5668	0.1367	-0.1291	0.1872	-0.12	0.0063	0.2277	0.0239	0.2346	11.985	38.664	-13.297
4	1.3828	0.4194	0.0751	0.5962	0.0707	0.7605	-0.0571	0.0898	-0.0537	-0.0972	0.0359	0.0563	-0.0048	-0.0595	0.0212	0.0177	0.0036	-0.014	0.1187	0.0074	0.0444	-10.853	20.323	-22.505
5	5.41	0.9542	-1.5024	3.9291	2.8493	8.1926	-0.0066	-0.1141	0.124	0.2979	-0.1271	0.1569	-0.0807	-0.2861	0.1338	0.0853	-0.0055	-0.0026	0.1195	0.0356	0.038	-18.302	20.168	-5.507
6	2.9857	0.5685	-1.0061	2.6233	-0.0648	1.3906	-0.0653	0.119	-0.3279	0.0054	0.0227	0.1591	0.1683	-0.0145	0.0425	0.029	0.0194	-0.0089	0.1153	-0.014	0.0729	-17.515	11.873	-21.685
7	2.9901	1.7233	-0.5641	9.8021	-1.8341	1.8478	-0.1113	0.2998	-0.2521	-0.1871	0.0722	-0.0354	0.1065	0.0259	0.0391	0.0642	-0.008	0.0199	0.2324	-0.0436	0.1193	1.076	16.129	-35.711
8	1.8757	0.2166	-0.6786	0.9679	-1.2066	2.6266	0.0288	-0.0301	0.05	-0.0232	0.0275	-0.0143	-0.1472	0.0194	-0.0564	0.04	-0.0192	0.0389	0.1424	0.0017	0.0795	17.399	25.026	-29.335
9	4.5479	-1.7156	-3.2633	4.9016	2.2493	6.9748	-0.2085	0.1153	-0.2162	0.3477	0.0734	0.1305	0.6977	-0.4866	0.1351	0.1022	-0.051	0.0239	0.139	0.0299	0.116	14.284	9.405	-17.197
10	2.671	-0.4474	-0.505	5.0082	-0.1126	4.9408	-0.1524	0.3039	0.0687	-0.358	0.0075	-0.6873	0.3098	0.1528	0.1448	0.1309	-0.0206	0.067	0.1627	0.0323	0.2011	22.596	8	-23.978
11	3.4662	-0.5956	0.2049	1.7464	0.0438	2.05	-0.0222	-0.1667	0.0767	0.0668	0.0143	0.2815	-0.2086	-0.1475	0.0078	0.0616	-0.0382	0.0371	0.159	-0.0121	0.0873	1.029	32.206	-11.62
12	5.3107	0.3646	1.6461	2.3557	0.7126	3.5319	-0.0397	-0.3676	0.5207	-0.0605	-0.1256	0.4489	-0.3224	-0.5124	0.1653	0.0434	0.0525	-0.0103	0.1831	-0.0291	0.1433	-13.199	35.361	-12.336
13	3.2166	0.2262	-1.1545	2.6774	1.4156	6.5343	0.0983	0.0042	0.1161	-0.2259	0.0392	-0.3192	-0.6229	0.3799	-0.1374	0.0712	-0.026	0.0403	0.1256	-0.0031	0.0802	11.746	36.343	-15.769
14	2.0606	0.9091	-3.9105	0.9914	-1.1545	7.9793	0.1539	0.015	0.015	-0.0718	-0.0176	-0.123	-0.4004	-0.0559	-0.1363	0.184	-0.0038	0.0456	0.2126	0.0305	0.2059	5.334	40.988	4.596

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 14
2	X-RAY DIFFRACTION	2	A	15 - 28
3	X-RAY DIFFRACTION	3	A	29 - 47
4	X-RAY DIFFRACTION	4	A	48 - 128
5	X-RAY DIFFRACTION	5	A	129 - 152
6	X-RAY DIFFRACTION	6	A	153 - 209
7	X-RAY DIFFRACTION	7	A	210 - 225
8	X-RAY DIFFRACTION	8	A	226 - 289
9	X-RAY DIFFRACTION	9	A	290 - 307
10	X-RAY DIFFRACTION	10	A	308 - 332
11	X-RAY DIFFRACTION	11	A	333 - 421
12	X-RAY DIFFRACTION	12	A	422 - 455
13	X-RAY DIFFRACTION	13	A	456 - 477
14	X-RAY DIFFRACTION	14	A	478 - 488

+
About Yorodumi

-
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