[English] 日本語
Yorodumi
- PDB-1gpj: Glutamyl-tRNA Reductase from Methanopyrus kandleri -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gpj
TitleGlutamyl-tRNA Reductase from Methanopyrus kandleri
ComponentsGlutamyl-tRNA reductase
KeywordsREDUCTASE / TRNA-DEPENDENT TETRAPYRROLE BIOSYNTHESIS / GLUTAMYL TRNA- REDUCTASE
Function / homology
Function and homology information


glutamyl-tRNA reductase / glutamyl-tRNA reductase activity / protoporphyrinogen IX biosynthetic process / NADP binding
Similarity search - Function
Glutamyl tRNA-reductase dimerization domain / Glutamyl-tRNA reductase, N-terminal domain / Glutamyl-tRNA reductase / Glutamyl-tRNA reductase, N-terminal / Tetrapyrrole biosynthesis, glutamyl-tRNA reductase, dimerisation domain / Glutamyl-tRNA reductase, conserved site / Glutamyl-tRNA reductase, N-terminal domain superfamily / Glutamyl tRNA-reductase dimerization domain superfamily / Glutamyl-tRNAGlu reductase, dimerisation domain / Glutamyl-tRNAGlu reductase, N-terminal domain ...Glutamyl tRNA-reductase dimerization domain / Glutamyl-tRNA reductase, N-terminal domain / Glutamyl-tRNA reductase / Glutamyl-tRNA reductase, N-terminal / Tetrapyrrole biosynthesis, glutamyl-tRNA reductase, dimerisation domain / Glutamyl-tRNA reductase, conserved site / Glutamyl-tRNA reductase, N-terminal domain superfamily / Glutamyl tRNA-reductase dimerization domain superfamily / Glutamyl-tRNAGlu reductase, dimerisation domain / Glutamyl-tRNAGlu reductase, N-terminal domain / Glutamyl-tRNA reductase signature. / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Beta Polymerase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / GLUTAMIC ACID / Chem-GMC / Glutamyl-tRNA reductase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.95 Å
AuthorsMoser, J. / Schubert, W.-D. / Beier, V. / Bringemeier, I. / Jahn, D. / Heinz, D.W.
CitationJournal: EMBO J. / Year: 2001
Title: V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis.
Authors: Moser, J. / Schubert, W.D. / Beier, V. / Bringemeier, I. / Jahn, D. / Heinz, D.W.
History
DepositionNov 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 7, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamyl-tRNA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0734
Polymers45,4401
Non-polymers6343
Water6,359353
1
A: Glutamyl-tRNA reductase
hetero molecules

A: Glutamyl-tRNA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1468
Polymers90,8792
Non-polymers1,2676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.267, 98.650, 68.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2021-

HOH

21A-2127-

HOH

-
Components

#1: Protein Glutamyl-tRNA reductase / / GluTR


Mass: 45439.516 Da / Num. of mol.: 1 / Fragment: WHOLE MOLECULE, RESIDUES 1-404 / Mutation: Cys to Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea)
Description: DSM 6324, GERMAN COLLECTION OF MICROORGANISMS (DSM)
Gene: hemA, MK0200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UXR8, glutamyl-tRNA reductase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-GMC / (2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL / 6N-DIMETHYL-3'-DEOXY-AMINO-ADENOSINE


Mass: 294.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N6O3
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALL CYSTEINES REPLACED BY SERINE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: METHOD: HANGING DROP, TEMP.: 4C, PROTEIN CONCENTRATION: 9.8 MG/ML, PRECIPITANT: 30 MPD, BUFFER: 100MM HEPES PH 7.5, SALT: 200MM NACL, 200MM NACITRATE, 2MM MGCL2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19.6 mg/mlprotein1drop
20.2 M1reservoirNaCl
32 mM1reservoirMgCl2
4100 mMHEPES1reservoirpH7.5
50.2 Msodium citrate1reservoir
630 %(v/v)MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→30.7 Å / Num. obs: 32681 / % possible obs: 91.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.2 / % possible all: 69.1
Reflection shell
*PLUS
% possible obs: 69.1 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
SOLOMONphasing
RefinementMethod to determine structure: MIR / Resolution: 1.95→69 Å / SU B: 7.199 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R Free: 0.191
Details: RESIDUES 356-360 ARE NOT VISIBLE AND ARE NOT MODELLED. NEIGBOURING REGIONS AS WELL AS RESIDUES 384- 390 HAVE POORLY DEFINED STEREOCHEMISTY.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1641 5.1 %RANDOM
Rwork0.212 ---
obs-30507 91.1 %-
Refinement stepCycle: LAST / Resolution: 1.95→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 43 353 3544
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3

+
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