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- PDB-1ges: ANATOMY OF AN ENGINEERED NAD-BINDING SITE -

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Basic information

Entry
Database: PDB / ID: 1ges
TitleANATOMY OF AN ENGINEERED NAD-BINDING SITE
ComponentsGLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE(FLAVOENZYME)
Function / homology
Function and homology information


glutathione-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / FAD binding / cell redox homeostasis / flavin adenine dinucleotide binding / NADP binding / cellular response to oxidative stress / membrane / cytosol
Similarity search - Function
Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily ...Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Glutathione reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.74 Å
AuthorsMittl, P.R.E. / Schulz, G.E.
Citation
Journal: Protein Sci. / Year: 1994
Title: Anatomy of an engineered NAD-binding site.
Authors: Mittl, P.R. / Berry, A. / Scrutton, N.S. / Perham, R.N. / Schulz, G.E.
#1: Journal: Protein Sci. / Year: 1994
Title: The Structure of Glutathione Reductase from Escherichia Coli at 1.86 Angstroms Resolution: Comparison with the Enzyme from Human Erythrocytes
Authors: Mittl, P.R.E. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Structural Differences between Wild-Type Nad-Dependent Glutathione Reductase from Escherichia Coli and a Redesigned Nad-Dependent Mutant
Authors: Mittl, P.R.E. / Berry, A. / Scrutton, N.S. / Perham, R.N. / Schulz, G.E.
#3: Journal: Nature / Year: 1990
Title: Redesign of the Cofactor Specificity of a Dehydrogenase by Protein Engineering
Authors: Scrutton, N.S. / Berry, A. / Perham, R.N.
History
DepositionJan 18, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: 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 / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE REDUCTASE
B: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0494
Polymers97,4782
Non-polymers1,5712
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-71 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.000, 72.800, 61.000
Angle α, β, γ (deg.)90.00, 90.00, 82.80
Int Tables number4
Space group name H-MP1121
Atom site foot note1: CIS PROLINE - PRO A 223 / 2: CIS PROLINE - PRO A 347 / 3: CIS PROLINE - PRO A 440 / 4: CIS PROLINE - PRO B 223 / 5: CIS PROLINE - PRO B 347 / 6: CIS PROLINE - PRO B 440
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.996127, 0.010365, -0.087312), (-0.018507, -0.995497, 0.092969), (-0.085955, 0.094225, 0.991833)
Vector: 59.728, 1.05, 2.586)
DetailsTHERE IS A WHOLE DIMER IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT, THE SUBUNITS ARE MARKED BY DIFFERENT SEGMENT IDS, NAMELY CHAINS A AND B. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein GLUTATHIONE REDUCTASE


Mass: 48739.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P06715, EC: 1.6.4.2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.74 Å / % possible obs: 94 % / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Highest resolution: 1.74 Å / Lowest resolution: 1.78 Å / % possible obs: 93 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.74→7 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.168 -
obs0.168 100974
Refinement stepCycle: LAST / Resolution: 1.74→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 106 585 7523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 100974 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.69

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