[English] 日本語
Yorodumi
- PDB-1aup: GLUTAMATE DEHYDROGENASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aup
TitleGLUTAMATE DEHYDROGENASE
ComponentsNAD-SPECIFIC GLUTAMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD
Function / homology
Function and homology information


glutamate catabolic process via 2-hydroxyglutarate / glutamate dehydrogenase / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process / cytosol
Similarity search - Function
Glutamate Dehydrogenase, chain A, domain 3 / Glutamate Dehydrogenase; Chain A, domain 3 / Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain ...Glutamate Dehydrogenase, chain A, domain 3 / Glutamate Dehydrogenase; Chain A, domain 3 / Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NAD-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBaker, P.J. / Waugh, M.L. / Stillman, T.J. / Turnbull, A.P. / Rice, D.W.
Citation
Journal: Biochemistry / Year: 1997
Title: Determinants of substrate specificity in the superfamily of amino acid dehydrogenases.
Authors: Baker, P.J. / Waugh, M.L. / Wang, X.G. / Stillman, T.J. / Turnbull, A.P. / Engel, P.C. / Rice, D.W.
#1: Journal: Structure / Year: 1995
Title: The Structure of Pyrococcus Furiosus Glutamate Dehydrogenase Reveals a Key Role for Ion-Pair Networks in Maintaining Enzyme Stability at Extreme Temperatures
Authors: Yip, K.S. / Stillman, T.J. / Britton, K.L. / Artymiuk, P.J. / Baker, P.J. / Sedelnikova, S.E. / Engel, P.C. / Pasquo, A. / Chiaraluce, R. / Consalvi, V. / Scandurra, R. / Rice, D.W.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Conformational Flexibility in Glutamate Dehydrogenase. Role of Water in Substrate Recognition and Catalysis
Authors: Stillman, T.J. / Baker, P.J. / Britton, K.L. / Rice, D.W.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Erratum. Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity
Authors: Baker, P.J. / Britton, K.L. / Rice, D.W. / Rob, A. / Stillman, T.J.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity
Authors: Baker, P.J. / Britton, K.L. / Rice, D.W. / Rob, A. / Stillman, T.J.
#5: Journal: Eur.J.Biochem. / Year: 1992
Title: Structural Relationship between the Hexameric and Tetrameric Family of Glutamate Dehydrogenases
Authors: Britton, K.L. / Baker, P.J. / Rice, D.W. / Stillman, T.J.
#6: Journal: Proteins / Year: 1992
Title: Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase
Authors: Baker, P.J. / Britton, K.L. / Engel, P.C. / Farrants, G.W. / Lilley, K.S. / Rice, D.W. / Stillman, T.J.
#7: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallization of an Nad+-Dependent Glutamate Dehydrogenase from Clostridium Symbiosum
Authors: Rice, D.W. / Hornby, D.P. / Engel, P.C.
History
DepositionSep 1, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)49,2121
Polymers49,2121
Non-polymers00
Water72140
1
A: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
x 6


Theoretical massNumber of molelcules
Total (without water)295,2706
Polymers295,2706
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation5_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)162.900, 162.900, 100.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein NAD-SPECIFIC GLUTAMATE DEHYDROGENASE


Mass: 49211.676 Da / Num. of mol.: 1 / Mutation: K89L, S380V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: GDH / Plasmid: PTAC85/PTAC44 / Gene (production host): GDH / Production host: Escherichia coli (E. coli) / Strain (production host): Q100 / References: UniProt: P24295, glutamate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.6 Å3/Da / Density % sol: 52.9 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.0 Msodium glutamate1drop
30.1 Mpotassium phosphate1drop
40.1 Mpotassium phosphate1reservoir
538-46 %ammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 12, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.5→18 Å / Num. obs: 17791 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14 / Rsym value: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 99
Reflection
*PLUS
Num. measured all: 90734 / Rmerge(I) obs: 0.07

-
Processing

Software
NameVersionClassification
TFFCmodel building
TNT5Erefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TFFCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CLOSTRIDIUM SYMBIOSUM GLUTAMATE DEHYDROGENASE (WILD TYPE) CRYSTALLIZED WITH SODIUM GLUTAMATE IN SPACE GROUP R32. ALL WATERS AND THE BOUND GLUTAMATE SUBSTRATE REMOVED.

Resolution: 2.5→18 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rwork0.19 --
all-17791 -
obs-17791 99 %
Solvent computationSolvent model: MOEWS AND KRETSINGER / Bsol: 190 Å2 / ksol: 0.7 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 0 40 3315
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01733441.5
X-RAY DIFFRACTIONt_angle_deg1.345053
X-RAY DIFFRACTIONt_dihedral_angle_d18.619980
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01924
X-RAY DIFFRACTIONt_gen_planes0.0154879
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.15730.5
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.60
X-RAY DIFFRACTIONt_planar_d0.0192
X-RAY DIFFRACTIONt_plane_restr0.0159

+
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