[English] 日本語
Yorodumi
- PDB-5opo: Crystal structure of R238G cN-II mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5opo
TitleCrystal structure of R238G cN-II mutant
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE / nucleotidase / relapsed leukemia
Function / homology
Function and homology information


nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / : / GMP metabolic process / : / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host ...nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / : / GMP metabolic process / : / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / : / adenosine metabolic process / dGMP catabolic process / IMP-specific 5'-nucleotidase / IMP catabolic process / Ribavirin ADME / IMP metabolic process / 5'-nucleotidase / Purine catabolism / allantoin metabolic process / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase / Purine 5'-nucleotidase / 5' nucleotidase family / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHnizda, A. / Pachl, P. / Rezacova, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation15-06582S Czech Republic
CitationJournal: 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
DepositionAug 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7939
Polymers56,1241
Non-polymers6698
Water8,287460
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


Theoretical massNumber of molelcules
Total (without water)227,17236
Polymers224,4964
Non-polymers2,67632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area20170 Å2
ΔGint-73 kcal/mol
Surface area76780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.612, 126.862, 130.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Cytosolic purine 5'-nucleotidase / Cytosolic 5'-nucleotidase II


Mass: 56124.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P49902, 5'-nucleotidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / 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.: 460 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M MOPS/HEPES-Na pH 7.5; 0.03 M of each divalent cation ; 10% w/v PEG 4000, 20% v/v glycerol A7 Morpheus condition

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.894 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.894 Å / Relative weight: 1
ReflectionResolution: 1.969→48.43 Å / Num. obs: 54032 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 30.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.112 / Net I/σ(I): 13.6
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 4.58 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 8599 / CC1/2: 0.703 / Rrim(I) all: 0.849 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
XDSdata reduction
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K7Y

5k7y


Resolution: 2→48.43 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2100 4.1 %RANDOM
Rwork0.1708 ---
obs0.1721 49530 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.54 Å2 / Biso mean: 32.031 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 43 467 4368
Biso mean--55.4 30.12 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194082
X-RAY DIFFRACTIONr_bond_other_d00.023849
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9665518
X-RAY DIFFRACTIONr_angle_other_deg3.58338883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26823.128195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02215713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5461527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024547
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02994
LS refinement shellResolution: 1.999→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 150 -
Rwork0.288 3552 -
all-3702 -
obs--99.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
18.31936.2999-0.5176.2575-0.78520.2529-0.00080.2459-0.4944-0.16530.0962-0.05390.23870.0274-0.09540.3857-0.0022-0.02850.2601-0.08010.2625-5.268-38.215-30.96
210.755911.31755.536212.2524.43838.89790.2285-0.1746-0.97980.0185-0.1941-1.02381.24280.0141-0.03430.4770.04670.10260.3441-0.03030.7537-11.155-47.199-22.052
31.66980.37680.16050.4717-0.0350.9047-0.03290.10640.0336-0.07350.0275-0.00830.04660.04710.00540.0590.00880.0110.0235-0.00790.01396.565-22.457-20.731
45.27863.3154-1.76484.8092-0.79969.1392-0.1236-0.0266-0.41810.0658-0.0849-0.47040.54540.70510.20860.16480.0154-0.00120.10430.00370.061621.47-22.921-4.882
53.45761.27660.67882.62820.41642.0927-0.10630.17130.25230.01040.0939-0.0578-0.07620.03410.01240.05390.02430.01140.03180.0250.045317.796-14.633-19.401
66.57550.74783.79352.52130.21022.96530.0103-0.16170.3476-0.035-0.00350.1626-0.0475-0.2844-0.00690.11160.04970.03230.09740.02790.118312.919-7.211-21.906
74.16811.0193-0.81561.89070.20742.354-0.15390.4715-0.0046-0.1590.14160.00260.2267-0.15140.01220.1267-0.008-0.05370.10780.00310.0392-11.7-25.009-30.191
82.27180.97290.60831.34010.99372.0698-0.04860.149-0.0095-0.12120.04370.0112-0.04250.01250.00480.0663-0.0122-0.03780.0667-0.00550.0279-17.1-21.955-31.154
90.9061-0.82030.74292.8575-1.0421.6841-0.0954-0.06020.13740.00940.05890.1706-0.244-0.12180.03640.1023-0.0233-0.01760.1008-0.02640.0691-16.055-15.593-15.836
103.8547-2.83713.61863.6581-1.88795.30040.21680.152-0.42580.0292-0.1087-0.19580.86320.3209-0.1080.32380.05920.10180.1660.02660.412710.141-42.825-14.436
1129.793.1686-23.97581.0264-1.494120.9235-0.37570.78910.34810.1130.42610.17350.5148-0.1469-0.05040.28060.0616-0.09240.37210.04050.29926.966-47.149-0.197
122.63680.8354-0.74751.7106-0.24092.3117-0.0156-0.1612-0.2761-0.0982-0.0169-0.19150.2580.15810.03240.13280.02810.01010.02630.0060.04534.111-35.931-13.525
132.42811.29164.21560.72731.866111.36750.1079-0.0094-0.07170.03130.0192-0.02580.2046-0.1527-0.12710.18630.0131-0.02810.1397-0.01560.1712-5.218-40.9634.781
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 20
2X-RAY DIFFRACTION2A21 - 34
3X-RAY DIFFRACTION3A35 - 127
4X-RAY DIFFRACTION4A128 - 145
5X-RAY DIFFRACTION5A146 - 186
6X-RAY DIFFRACTION6A187 - 212
7X-RAY DIFFRACTION7A213 - 248
8X-RAY DIFFRACTION8A249 - 290
9X-RAY DIFFRACTION9A291 - 371
10X-RAY DIFFRACTION10A372 - 399
11X-RAY DIFFRACTION11A400 - 419
12X-RAY DIFFRACTION12A420 - 477
13X-RAY DIFFRACTION13A478 - 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://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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more