[English] 日本語
Yorodumi
- PDB-5yfx: Crystal structure of ribose-1,5-bisphosphate isomerase mutant D20... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yfx
TitleCrystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP
ComponentsRibose 1,5-bisphosphate isomerase
KeywordsISOMERASE / NMP degradation pathway / Ribose-1 / 5-bisphosphate / Rossmann-like fold
Function / homology
Function and homology information


ribose-1,5-bisphosphate isomerase / ribose 1,5-bisphosphate isomerase activity / S-methyl-5-thioribose-1-phosphate isomerase activity / pentose catabolic process / L-methionine salvage from methylthioadenosine
Similarity search - Function
Ribose-1,5-bisphosphate isomerase, e2b2 family / Initiation factor 2B alpha/beta/delta / translation initiation factor eif-2b, domain 1 / Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eif-2b; domain 2 / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Ribose-1,5-bisphosphate isomerase, e2b2 family / Initiation factor 2B alpha/beta/delta / translation initiation factor eif-2b, domain 1 / Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eif-2b; domain 2 / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 1,5-di-O-phosphono-alpha-D-ribofuranose / Ribose 1,5-bisphosphate isomerase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsGogoi, P. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT)BT/302/NE/TBP/2012 dated 07.01.2013 India
CitationJournal: Sci Rep / Year: 2018
Title: A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.
Authors: Gogoi, P. / Kanaujia, S.P.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribose 1,5-bisphosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1133
Polymers36,4551
Non-polymers6572
Water81145
1
A: Ribose 1,5-bisphosphate isomerase
hetero molecules
x 6


  • defined by author&software
  • Evidence: -0.500000 -0.866025 0.000000 121.69500 0.866025 -0.500000 0.000000 70.26064 0.000000 0.000000 1.000000 0.00000 -0.500000 -0.866025 0.000000 121.69500 -0.866025 0.500000 0.000000 70.26064 0. ...Evidence: -0.500000 -0.866025 0.000000 121.69500 0.866025 -0.500000 0.000000 70.26064 0.000000 0.000000 1.000000 0.00000 -0.500000 -0.866025 0.000000 121.69500 -0.866025 0.500000 0.000000 70.26064 0.000000 0.000000 -1.000000 0.00000 -0.500000 0.866025 0.000000 0.00000 -0.866025 -0.500000 0.000000 140.52128 0.000000 0.000000 1.000000 0.00000 1.000000 0.000000 0.000000 0.00000 0.000000 -1.000000 0.000000 140.52128 0.000000 0.000000 -1.000000 0.00000
  • 223 kDa, 6 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)222,67618
Polymers218,7326
Non-polymers3,94412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
Buried area27040 Å2
ΔGint-96 kcal/mol
Surface area64020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.130, 81.130, 100.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

-
Components

#1: Protein Ribose 1,5-bisphosphate isomerase


Mass: 36455.367 Da / Num. of mol.: 1 / Mutation: D204N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0208 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: O57947, ribose-1,5-bisphosphate isomerase
#2: Sugar ChemComp-RI2 / 1,5-di-O-phosphono-alpha-D-ribofuranose / 1,5-di-O-phosphono-alpha-D-ribose / 1,5-di-O-phosphono-D-ribose / 1,5-di-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 310.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O11P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.61 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.7 M NaCl, 3% PEG 6000, 20% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 23, 2016 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→100.18 Å / Num. obs: 10900 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.839.80.5414.414080.9520.1820.572100
9.10.0263550.9990.0090.02899.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.74 Å70.26 Å
Translation6.74 Å70.26 Å

-
Processing

Software
NameVersionClassification
HKL-3000data collection
MOSFLM7.2.1data processing
Aimless0.5.28data scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
Coot0.8.6model building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YFJ

5yfj


Resolution: 2.7→100.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.884 / SU B: 14.891 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 552 5.1 %RANDOM
Rwork0.1765 ---
obs0.1809 10348 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.85 Å2 / Biso mean: 48.382 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å2-0.93 Å2-0 Å2
2---1.85 Å20 Å2
3---6.02 Å2
Refinement stepCycle: final / Resolution: 2.7→100.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 41 45 2624
Biso mean--38.31 32.38 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192633
X-RAY DIFFRACTIONr_bond_other_d0.0020.022592
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.983570
X-RAY DIFFRACTIONr_angle_other_deg0.96135984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62424.135104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00215483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5811515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212847
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02547
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 21 -
Rwork0.285 758 -
all-779 -
obs--100 %

+
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