[English] 日本語
Yorodumi
- PDB-1sgv: STRUCTURE OF TRNA PSI55 PSEUDOURIDINE SYNTHASE (TRUB) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sgv
TitleSTRUCTURE OF TRNA PSI55 PSEUDOURIDINE SYNTHASE (TRUB)
ComponentstRNA pseudouridine synthase B
KeywordsLYASE / Hinged motion / tRNA modification / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / cell wall / RNA binding
Similarity search - Function
tRNA pseudouridine synthase II, TruB, subfamily 2, C-terminal / tRNA Pseudouridine synthase II, C terminal / tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain ...tRNA pseudouridine synthase II, TruB, subfamily 2, C-terminal / tRNA Pseudouridine synthase II, C terminal / tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA domain superfamily / PUA-like superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
tRNA pseudouridine synthase B / tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChaudhuri, B.N. / Chan, S. / Perry, L.J. / Yeates, T.O. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft.
Authors: Chaudhuri, B.N. / Chan, S. / Perry, L.J. / Yeates, T.O.
History
DepositionFeb 24, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionMar 2, 2004ID: 1S71
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA pseudouridine synthase B
B: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)67,7222
Polymers67,7222
Non-polymers00
Water8,125451
1
A: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)33,8611
Polymers33,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)33,8611
Polymers33,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.948, 94.100, 78.508
Angle α, β, γ (deg.)90.00, 100.36, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein tRNA pseudouridine synthase B / tRNA pseudouridine 55 synthase / Psi55 synthase / Pseudouridylate synthase / Uracil hydrolyase


Mass: 33860.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: TRUB, RV2793C, MT2862.1, MTV002.58C, MB2816C / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-GOLD
References: UniProt: P62190, UniProt: P9WHP7*PLUS, pseudouridylate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 3.03 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 298 K / Method: microseeding / pH: 7.5
Details: AMMONIUM SULFATE, TRIS BUFFER, PEG3350, pH 7.5, temperature 298K, microseeding
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH8.
20.3 M1dropNaCl
320 mg/mlprotein1drop
40.2 Mammonium sulfate1reservoir
50.1 MTris1reservoirpH8.5
625 %(w/v)PEG33501reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.0322 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0322 Å / Relative weight: 1
ReflectionResolution: 1.9→40.2 Å / Num. obs: 51411 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % possible obs: 99.5 % / Redundancy: 3.6 % / Num. measured all: 184403
Reflection shell
*PLUS
% possible obs: 99.5 % / Redundancy: 3.2 % / Mean I/σ(I) obs: 2

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K8W protein component

1k8w


Resolution: 1.9→40.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.491 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23947 2551 5 %RANDOM
Rwork0.20082 ---
obs0.20268 48859 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.756 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.35 Å2
2---0.43 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 0 451 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213963
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.9775359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022958
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.21772
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3871.52607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74924150
X-RAY DIFFRACTIONr_scbond_it1.25431356
X-RAY DIFFRACTIONr_scangle_it2.2584.51209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 182
Rwork0.28 3521
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)
12.6396-0.4657-2.31483.54391.88373.58840.23610.11230.322-0.75560.2168-0.5189-0.58070.0578-0.45280.256-0.03410.07230.1656-0.00860.160815.349-1.20525.371
23.9918-1.5462-1.8913.05371.11112.58420.07940.10920.0865-0.14180.01990.0934-0.05050.0046-0.09940.02380.013-0.04370.15830.020.1207-6.7583.98343.054
32.54810.52481.29547.89341.15995.40840.01350.43110.0949-1.25-0.0749-0.4293-0.0680.26170.06140.425-0.00390.10460.2329-0.01630.102915.546-21.79711.223
41.8267-0.29360.58493.519-0.78642.5150.0351-0.0604-0.16790.22160.09390.23550.0831-0.1744-0.1290.03510.0082-0.02560.1870.03460.0783-25.841.43255.738
53.3709-2.16323.41593.0932-3.52657.69190.02570.19110.03490.1507-0.0076-0.06830.0570.1773-0.01810.39570.0066-0.0510.24580.03490.0414-12.141-1.68681.034
63.3805-0.4302-1.06149.58490.46944.12230.06250.2676-0.1083-0.6904-0.0115-0.0416-0.1021-0.0294-0.0510.13420.0382-0.02530.14630.02310.0507-22.97622.36342.285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 713 - 71
2X-RAY DIFFRACTION1AA200 - 226200 - 226
3X-RAY DIFFRACTION2AA72 - 19972 - 199
4X-RAY DIFFRACTION3AA227 - 292227 - 292
5X-RAY DIFFRACTION4BB1 - 711 - 71
6X-RAY DIFFRACTION4BB200 - 226200 - 226
7X-RAY DIFFRACTION5BB72 - 19972 - 199
8X-RAY DIFFRACTION6BB227 - 294227 - 294
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40.2 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.97
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg5.5
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.95 Å / Rfactor Rfree: 0.33

+
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