[English] 日本語
Yorodumi
- PDB-5opp: Crystal structure of S408R cN-II mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5opp
TitleCrystal structure of S408R cN-II mutant
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE / 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 ...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 / IMP metabolic process / Ribavirin ADME / IMP catabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
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
BROMIDE ION / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 9, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
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)56,6056
Polymers56,2241
Non-polymers3805
Water4,432246
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)226,41924
Polymers224,8974
Non-polymers1,52220
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 area16000 Å2
ΔGint-80 kcal/mol
Surface area77210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.668, 127.025, 130.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-825-

HOH

-
Components

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


Mass: 56224.180 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 BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P49902, 5'-nucleotidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / 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: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 63.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M bicine/Trizma base pH 8.5; 0.03 M of each halide; 10% w/v PEG 8000, 20% v/v ethylene glycol B10 Morpheus condition

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.698→45.83 Å / Num. obs: 82606 / % possible obs: 98.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.065 / Net I/σ(I): 13.7
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 12777 / CC1/2: 0.486 / Rrim(I) all: 0.861 / % possible all: 95.2

-
Processing

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

5k7y


Resolution: 1.7→45.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.084
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2100 2.5 %RANDOM
Rwork0.191 ---
obs0.1916 80506 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.54 Å2 / Biso mean: 36.503 Å2 / Biso min: 12.99 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 20 246 4097
Biso mean--52.46 35.95 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193988
X-RAY DIFFRACTIONr_bond_other_d00.023747
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9615391
X-RAY DIFFRACTIONr_angle_other_deg3.61338636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7423.141191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87415692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.621526
X-RAY DIFFRACTIONr_chiral_restr0.0940.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024458
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02978
LS refinement shellResolution: 1.698→1.742 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 140 -
Rwork0.395 5386 -
all-5526 -
obs--90.13 %
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)
18.3842-7.8653-2.38617.40742.20471.0858-0.1061-0.1299-0.18020.13270.17620.16580.2632-0.2117-0.07010.2782-0.0715-0.06680.19580.07050.11445.124-38.36230.913
21.89045.79393.911819.323812.93048.8459-0.51990.06270.3264-0.64990.03191.0537-0.43790.14030.4880.476-0.0056-0.06740.24130.1490.364213.467-48.66722.669
31.52230.20451.39570.04610.18531.56990.28250.1692-0.0450.0371-0.0411-0.00040.33380.1207-0.24130.08450.0418-0.04630.20460.01230.13312.968-33.88714.638
41.204-0.33850.07140.33770.31290.5176-0.0638-0.09280.02540.01570.01450.02090.0258-0.03850.04920.0248-0.0070.0160.13840.00270.0647-12.886-19.822.641
52.7473-0.04620.07552.6262.70454.86690.05590.1769-0.1335-0.1586-0.1447-0.0386-0.0521-0.24150.08880.0458-0.0142-0.0090.13170.01630.0277-18.86-20.2095.217
63.0752-0.99980.93041.72420.11911.054-0.0985-0.18830.17910.0380.03310.113-0.0306-0.01580.06540.013-0.00960.0110.0929-0.010.0849-18.54-15.39721.717
74.3763-1.8071.711.2927-0.63080.9602-0.1469-0.26670.39320.03310.0922-0.0496-0.11840.03860.05460.0193-0.02730.00160.1456-0.06430.1138-7.603-11.96827.449
81.54470.02910.55910.729-0.50782.05510.03260.03620.11410.055-0.0081-0.0690.1303-0.0274-0.02440.03560.0286-0.03310.13230.00740.081917.402-23.83428.353
90.171-0.38850.62015.4353-0.95923.3872-0.1862-0.0816-0.0709-0.00730.2826-0.53-0.9514-0.3104-0.09640.30090.0770.04810.04860.02620.286820.424-8.12121.345
102.38230.8473-0.29730.4636-0.89283.9325-0.04870.13740.28590.0220.03190.0977-0.18730.1430.01680.0180.0215-0.00760.220.02940.112715.272-22.04912.389
110.36930.42770.45640.60550.61810.68730.0313-0.05410.09110.1345-0.09810.08280.1543-0.01580.06680.10140.0449-0.00140.17810.01290.0626-3.527-36.2711.889
122.06710.0398-0.91511.81740.11751.87040.04520.285-0.25320.1041-0.12840.29250.2117-0.29660.08320.058-0.0550.02030.1794-0.04020.1244-14.619-35.95911.568
132.1604-0.30011.27420.72040.93433.71360.0750.0769-0.01140.1660.0275-0.0690.35880.1899-0.10240.07180.02-0.04040.1112-0.00220.053311.634-36.09215.786
143.19440.63546.07540.17921.328511.86020.4393-0.0712-0.11460.06070.0139-0.1160.7517-0.1411-0.45320.17050.0153-0.00490.16460.0110.22145.111-40.808-4.771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 20
2X-RAY DIFFRACTION2A21 - 30
3X-RAY DIFFRACTION3A31 - 54
4X-RAY DIFFRACTION4A55 - 128
5X-RAY DIFFRACTION5A129 - 151
6X-RAY DIFFRACTION6A152 - 185
7X-RAY DIFFRACTION7A186 - 228
8X-RAY DIFFRACTION8A229 - 293
9X-RAY DIFFRACTION9A294 - 333
10X-RAY DIFFRACTION10A334 - 357
11X-RAY DIFFRACTION11A358 - 418
12X-RAY DIFFRACTION12A419 - 455
13X-RAY DIFFRACTION13A456 - 477
14X-RAY DIFFRACTION14A478 - 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