[English] 日本語
Yorodumi
- PDB-5tsq: Crystal structure of IUnH from Leishmania braziliensis in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tsq
TitleCrystal structure of IUnH from Leishmania braziliensis in complex with D-Ribose
ComponentsIUnH
KeywordsHYDROLASE / IUnH / Leishmania braziliensis / D-Ribose
Function / homology
Function and homology information


uridine nucleosidase activity / nucleobase-containing compound metabolic process / metal ion binding
Similarity search - Function
Inosine/uridine-preferring nucleoside hydrolase, conserved site / Inosine-uridine preferring nucleoside hydrolase family signature. / Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
beta-D-ribofuranose / Nonspecific nucleoside hydrolasewith=GeneDB:LmjF18.1580
Similarity search - Component
Biological speciesLeishmania braziliensis braziliensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsBachega, J.F.R. / Timmers, L.F.S.M. / Dalberto, P.F. / Martinelli, L. / Pinto, A.F.M. / Basso, L.A. / Norberto de Souza, O. / Santos, D.S.
CitationJournal: To Be Published
Title: Crystal structure of IUnH from Leishmania braziliensis in complex with D-Ribose
Authors: Bachega, J.F.R. / Timmers, L.F.S.M. / Dalberto, P.F. / Martinelli, L. / Pinto, A.F.M. / Basso, L.A. / Norberto de Souza, O. / Santos, D.S.
History
DepositionOct 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IUnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4393
Polymers34,2491
Non-polymers1902
Water5,008278
1
A: IUnH
hetero molecules

A: IUnH
hetero molecules

A: IUnH
hetero molecules

A: IUnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,75512
Polymers136,9944
Non-polymers7618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area9650 Å2
ΔGint-108 kcal/mol
Surface area44160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.660, 94.080, 123.120
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-507-

HOH

21A-564-

HOH

31A-702-

HOH

-
Components

#1: Protein IUnH


Mass: 34248.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis braziliensis (eukaryote)
Gene: LBRM_18_1610 / Production host: Escherichia coli (E. coli) / References: UniProt: A4H9Q9, purine nucleosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-BDR / beta-D-ribofuranose / beta-D-ribose / D-ribose / ribose / BETA-D-RIBOFURANOSYL


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribofuranoseCOMMON NAMEGMML 1.0
b-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium acetate, 0.1M HEPES pH 7.5 and 45% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.53→74.754 Å / Num. obs: 64501 / % possible obs: 98.5 % / Redundancy: 4.3 % / Rsym value: 0.091 / Net I/av σ(I): 4.421 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.53-1.612.30.4310.7190.8
1.61-1.713.20.3051199.3
1.71-1.833.70.2291.4199.7
1.83-1.984.60.14931100
1.98-2.165.10.1642.9199.9
2.16-2.425.20.1443.61100
2.42-2.795.20.1294.41100
2.79-3.425.30.0986.31100
3.42-4.845.50.04710.91100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.547
Highest resolutionLowest resolution
Rotation21.66 Å1.68 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
MOLREP11.2.08phasing
PHENIX1.11rc2_2531refinement
PDB_EXTRACT3.2data extraction
MOSFLM7.1.1data reduction
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZR

1ezr


Resolution: 1.53→21.655 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.52
RfactorNum. reflection% reflection
Rfree0.1685 3226 5.03 %
Rwork0.1534 --
obs0.1542 64118 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.82 Å2 / Biso mean: 24.5624 Å2 / Biso min: 8.2 Å2
Refinement stepCycle: final / Resolution: 1.53→21.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 11 278 2687
Biso mean--19.36 38.51 -
Num. residues----312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112490
X-RAY DIFFRACTIONf_angle_d0.9723395
X-RAY DIFFRACTIONf_chiral_restr0.062414
X-RAY DIFFRACTIONf_plane_restr0.007434
X-RAY DIFFRACTIONf_dihedral_angle_d4.712085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.55280.2881140.27192144X-RAY DIFFRACTION80
1.5528-1.57710.26351160.26032339X-RAY DIFFRACTION87
1.5771-1.60290.25021320.2382602X-RAY DIFFRACTION96
1.6029-1.63060.22051590.21482580X-RAY DIFFRACTION97
1.6306-1.66020.22011440.20192628X-RAY DIFFRACTION98
1.6602-1.69210.18421270.18652621X-RAY DIFFRACTION98
1.6921-1.72670.22431450.18972605X-RAY DIFFRACTION97
1.7267-1.76420.18531520.17452610X-RAY DIFFRACTION97
1.7642-1.80520.15181400.15692644X-RAY DIFFRACTION100
1.8052-1.85030.21591140.15062720X-RAY DIFFRACTION100
1.8503-1.90030.1531410.15052679X-RAY DIFFRACTION100
1.9003-1.95620.19481400.15642715X-RAY DIFFRACTION100
1.9562-2.01930.13951280.14212673X-RAY DIFFRACTION100
2.0193-2.09140.14911400.14792718X-RAY DIFFRACTION100
2.0914-2.17510.16881400.14432679X-RAY DIFFRACTION100
2.1751-2.2740.17061570.14392693X-RAY DIFFRACTION100
2.274-2.39370.16081510.14582705X-RAY DIFFRACTION100
2.3937-2.54350.19381410.15272700X-RAY DIFFRACTION100
2.5435-2.73950.18921550.14782703X-RAY DIFFRACTION100
2.7395-3.01450.14061450.13952728X-RAY DIFFRACTION100
3.0145-3.44920.13331660.13822738X-RAY DIFFRACTION100
3.4492-4.33990.13961540.12622755X-RAY DIFFRACTION100
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)
10.773-0.12010.4742.1816-0.46152.13670.0201-0.1124-0.16020.16270.0159-0.11120.34160.1336-0.00850.220.0368-0.04450.14580.0260.12539.265818.590919.3089
21.4407-0.39740.33651.8613-0.22581.75650.0559-0.0197-0.15570.0482-0.0397-0.2510.36740.2391-0.02950.20760.048-0.03830.1440.01370.13598.499418.709812.3121
30.6815-0.22570.11411.1849-0.18831.3419-0.0232-0.1096-0.04830.12470.0379-0.03840.0818-0.0275-0.03560.12650.0005-0.01750.12250.01960.07321.952129.556317.9416
42.1179-0.83680.07442.9305-0.29021.5824-0.0055-0.11010.27620.1534-0.0468-0.4982-0.12260.42350.33320.29340.0472-0.14690.35280.03030.255520.384729.045627.0063
50.7969-0.23860.2751.8172-0.70361.4688-0.0156-0.231-0.0530.29040.08520.05470.023-0.1049-0.03410.18480.003-0.00010.1730.01270.0755-0.413832.706824.62
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 56 )A2 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 129 )A57 - 129
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 212 )A130 - 212
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 233 )A213 - 233
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 313 )A234 - 313

+
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