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- PDB-1gpj: Glutamyl-tRNA Reductase from Methanopyrus kandleri -

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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 from glutamate / 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
Revision 1.6May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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


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

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Experimental details

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Experiment

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

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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

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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 %

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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

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