[English] 日本語
Yorodumi
- PDB-1usl: Structure Of Mycobacterium tuberculosis Ribose-5-Phosphate Isomer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1usl
TitleStructure Of Mycobacterium tuberculosis Ribose-5-Phosphate Isomerase, RpiB, Rv2465c, Complexed With Phosphate.
ComponentsRIBOSE 5-PHOSPHATE ISOMERASE B
KeywordsISOMERASE / PHOSPHOPENTOSE ISOMERASE B / PENTOSE PHOSPHATE PATHWAY / RV2465C / PHOSPHORIBOISOMERASE B / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


D-allose catabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / extracellular region
Similarity search - Function
Ribose 5-phosphate isomerase B, Actinobacteria-type / Sugar-phosphate isomerase, RpiB/LacA/LacB family / Sugar-phosphate isomerase, RpiB/LacA/LacB superfamily / Ribose/Galactose Isomerase / Ribose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / : / Ribose-5-phosphate isomerase B
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsRoos, A.K. / Andersson, C.E. / Unge, T. / Jones, T.A. / Mowbray, S.L.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Mycobacterium Tuberculosis Ribose-5-Phosphate Isomerase Has a Known Fold, But a Novel Active Site
Authors: Roos, A.K. / Andersson, C.E. / Bergfors, T. / Jacobsson, M. / Karlen, A. / Unge, T. / Jones, T.A. / Mowbray, S.L.
History
DepositionNov 25, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 6, 2020Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.5Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBOSE 5-PHOSPHATE ISOMERASE B
B: RIBOSE 5-PHOSPHATE ISOMERASE B
C: RIBOSE 5-PHOSPHATE ISOMERASE B
D: RIBOSE 5-PHOSPHATE ISOMERASE B
E: RIBOSE 5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,12810
Polymers91,6535
Non-polymers4755
Water10,431579
1
A: RIBOSE 5-PHOSPHATE ISOMERASE B
B: RIBOSE 5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8514
Polymers36,6612
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: RIBOSE 5-PHOSPHATE ISOMERASE B
D: RIBOSE 5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8514
Polymers36,6612
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: RIBOSE 5-PHOSPHATE ISOMERASE B
hetero molecules

E: RIBOSE 5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8514
Polymers36,6612
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)136.420, 102.390, 69.610
Angle α, β, γ (deg.)90.00, 95.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4097, 0.9078, 0.0896), (0.908, 0.3964, 0.1355), (0.0875, 0.1369, -0.9867)22.9439, -16.8527, 20.3123
2given(-0.3361, -0.9306, 0.1449), (-0.9299, 0.3036, -0.2074), (0.149, -0.2045, -0.9675)38.2994, 35.3876, 50.4059
3given(-0.691, 0.6428, -0.3305), (-0.6576, -0.7489, -0.0819), (-0.3002, 0.1607, 0.9403)43.5854, 38.8353, -21.3816
4given(-0.7701, -0.5427, -0.3353), (0.5343, -0.8359, 0.1259), (-0.3486, -0.0822, 0.9336)75.8417, -42.9673, 0.8567

-
Components

#1: Protein
RIBOSE 5-PHOSPHATE ISOMERASE B


Mass: 18330.672 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCR_T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: O53192, UniProt: P9WKD7*PLUS, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL 6-HIS TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.7 %
Crystal growpH: 7.5 / Details: 1.26 M NAKPO4 PH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.26 Msodium potassium phosphate1reservoirpH7.5
220 mg/mlprotein1drop
3150 mM1dropNaCl
420 mMMES1droppH6.
50.1 mMEDTA1drop
610 mMbeta-mercaptoethanol1drop
710 %glycerol1drop

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.098
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2002
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.098 Å / Relative weight: 1
ReflectionResolution: 1.88→81.65 Å / Num. obs: 73429 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.6
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.5 / % possible all: 90.6
Reflection
*PLUS
Highest resolution: 1.88 Å / Lowest resolution: 81.65 Å / Redundancy: 4.9 % / Num. measured all: 358802 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 90.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.5

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NN4

1nn4


Resolution: 1.88→81.65 Å / SU B: 2.581 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20182 3689 5 %RANDOM
Rwork0.16849 ---
obs0.17019 69739 95.49 %-
Displacement parametersBiso mean: 20.846 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.9 Å2
2---0.55 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.88→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5915 0 25 579 6519
Refinement
*PLUS
Rfactor Rfree: 0.202 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.167

+
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