[English] 日本語
Yorodumi
- PDB-1e5q: Ternary complex of saccharopine reductase from Magnaporthe grisea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e5q
TitleTernary complex of saccharopine reductase from Magnaporthe grisea, NADPH and saccharopine
ComponentsSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]
KeywordsOXIDOREDUCTASE / SACCHAROPINE REDUCTASE / NADPH / LYSINE BIOSYNTHESIS / ALPHA- AMINOADIPATE PATHWAY
Function / homology
Function and homology information


saccharopine dehydrogenase (NADP+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity / lysine biosynthetic process via aminoadipic acid / cytoplasm
Similarity search - Function
Domain 3, Saccharopine reductase / Domain 3, Saccharopine reductase / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Domain 3, Saccharopine reductase / Domain 3, Saccharopine reductase / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; 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
Chem-NDP / N-(5-AMINO-5-CARBOXYPENTYL)GLUTAMIC ACID / Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJohansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G.
CitationJournal: Structure / Year: 2000
Title: Crystal Structure of Saccharopine Reductase from Magnaporthe Grisea, an Enzyme of the Alpha-Aminoadipate Pathway of Lysine Biosynthesis
Authors: Johansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G.
History
DepositionJul 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description ..._diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
B: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
C: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
D: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
E: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
F: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
G: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
H: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,42424
Polymers393,2508
Non-polymers8,17416
Water45,2002509
1
A: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
B: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3566
Polymers98,3132
Non-polymers2,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
D: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3566
Polymers98,3132
Non-polymers2,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
F: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3566
Polymers98,3132
Non-polymers2,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
H: Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3566
Polymers98,3132
Non-polymers2,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.643, 205.809, 125.599
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.65256, -0.64454, 0.39841), (-0.66442, 0.23394, -0.7098), (0.36429, -0.7279, -0.58091)16.2141, 79.93341, 122.33724
2given(-0.65291, -0.64359, 0.39937), (0.67739, -0.26023, 0.68806), (-0.3389, 0.71977, 0.60587)59.04107, 42.97766, -1.46661
3given(0.99997, 0.00643, 0.00486), (0.00634, -0.99984, 0.01668), (0.00497, -0.01664, -0.99985)42.41738, 119.46846, 123.22049
4given(-0.64664, -0.65014, 0.39897), (0.67234, -0.23872, 0.70069), (-0.3603, 0.72134, 0.59149)4.93305, -38.29884, 62.16428
5given(0.99997, 0.005, -0.00504), (0.00499, -0.99999, -0.00182), (-0.00505, 0.00179, -0.99999)-11.13299, 40.98387, 184.70789
6given(1, -0.00029, -0.003), (0.00029, 1, 0.00107), (0.003, -0.00107, 0.99999)54.21876, 126.08662, -61.24036
7given(-0.64883, -0.64662, 0.40113), (-0.66685, 0.22926, -0.70905), (0.36653, -0.72754, -0.57995)70.05755, 206.20409, 61.11735

-
Components

#1: Protein
Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] / Saccharopine reductase


Mass: 49156.262 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: LYS3, MGG_08564 / Plasmid: PDB45 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FM5/PDB45
References: UniProt: Q9P4R4, saccharopine dehydrogenase (NADP+, L-glutamate-forming)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-SHR / N-(5-AMINO-5-CARBOXYPENTYL)GLUTAMIC ACID


Type: L-peptide linking / Mass: 276.286 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H20N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2509 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDESCRIBED IN JOHANSSON ET AL.(2000) ACTA CRYST. D56 662-664

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.25
Details: 8 MG/ML PROTEIN, 1 MM SACCHAROPINE, 1 MM NADPH, 20 % (W/W) PEG8000, 0.1 M TRIS-HCL PH 7.25, 1 MM DTT
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
21 mMNADPH1drop
39 mMsaccharopine1drop
420 %(w/w)PEG80001reservoir
50.1 MTris-HCl1reservoir
61 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8424 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 250975 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 18
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.5 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 2072876
Reflection shell
*PLUS
% possible obs: 96.5 %

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF9

1ff9


Resolution: 2.1→19.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3423402.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 12322 4.9 %RANDOM
Rwork0.207 ---
obs0.207 250248 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4148 Å2 / ksol: 0.335216 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å20 Å23.69 Å2
2---4.22 Å20 Å2
3---8.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27528 0 536 2509 30573
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 2012 4.9 %
Rwork0.257 39135 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2XDICT_8089.PARWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE_TEST.PARAMSAC_TOP.TXT
X-RAY DIFFRACTION4SAC_PAR.TXTXDICT_8089.TOP
X-RAY DIFFRACTION5WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

+
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://pdbjlvh1.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