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- PDB-1f6m: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THIOREDOXIN REDUCTASE, THI... -

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Basic information

Entry
Database: PDB / ID: 1f6m
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN THIOREDOXIN REDUCTASE, THIOREDOXIN, AND THE NADP+ ANALOG, AADP+
Components
  • THIOREDOXIN 1
  • THIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / ALTERNATE CONFORMATION / TERNARY COMPLEX / DOMAIN MOTION / redox-active center / NADP / FAD / electron transport
Function / homology
Function and homology information


thioredoxin-disulfide reductase complex / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / DNA polymerase processivity factor activity / protein-disulfide reductase activity / removal of superoxide radicals / cell redox homeostasis / flavin adenine dinucleotide binding / cytosol / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / Pyridine nucleotide-disulphide oxidoreductase / : / Thioredoxin / Thioredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin, conserved site ...Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / Pyridine nucleotide-disulphide oxidoreductase / : / Thioredoxin / Thioredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / FAD/NAD(P)-binding domain / Thioredoxin domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-AMINOPYRIDINE-ADENINE DINUCLEOTIDE PHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLennon, B.W. / Williams Jr., C.H. / Ludwig, M.L.
Citation
Journal: Science / Year: 2000
Title: Twists in catalysis: alternating conformations of Escherichia coli thioredoxin reductase.
Authors: Lennon, B.W. / Williams Jr., C.H. / Ludwig, M.L.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of Escherichia coli thioredoxin reductase refined at 2 A resolution. Implications for a large conformational change during catalysis.
Authors: Waksman, G. / Krishna, T.S. / Sweet, R.M. / Williams Jr., C.H. / Kuriyan, J.
#2: Journal: Nature / Year: 1991
Title: Convergent evolution of similar function in two structurally divergent enzymes
Authors: Kuriyan, J. / Krishna, T.S. / Wong, L. / Guenther, B. / Pahler, A. / Williams Jr., C.H. / Model, P.
History
DepositionJun 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details
Revision 1.7Nov 6, 2024Group: Structure summary / Category: 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: THIOREDOXIN REDUCTASE
B: THIOREDOXIN REDUCTASE
C: THIOREDOXIN 1
D: THIOREDOXIN 1
E: THIOREDOXIN REDUCTASE
F: THIOREDOXIN REDUCTASE
G: THIOREDOXIN 1
H: THIOREDOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,74816
Polymers184,7408
Non-polymers6,0088
Water4,252236
1
A: THIOREDOXIN REDUCTASE
B: THIOREDOXIN REDUCTASE
C: THIOREDOXIN 1
D: THIOREDOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3748
Polymers92,3704
Non-polymers3,0044
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-56 kcal/mol
Surface area32910 Å2
MethodPISA
2
E: THIOREDOXIN REDUCTASE
F: THIOREDOXIN REDUCTASE
G: THIOREDOXIN 1
H: THIOREDOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3748
Polymers92,3704
Non-polymers3,0044
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13730 Å2
ΔGint-55 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)298.929, 94.828, 79.613
Angle α, β, γ (deg.)90.00, 104.175, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4
DetailsThe biological assembly of thioreodxin reductase is a dimer consisting of chains A and B (corresponding to thioredoxin reductase chains B and A in the primary citation). This structure includes one FAD cofactor and one pyridine nucleotide product analog (AADP+) molecule per enzyme chain. The corresponding covalently bound thioredoxin substrate molecules (one per enzyme monomer) are chains C and D (corresponding to thioredoxin chains B and A in the primary citation). / The biological assembly of thioredoxin reductase is a dimer consisting of chains E and F (corresponding to thioredoxin reductase chains D and C in the primary citation). This structure includes one FAD cofactor and one pyridine nucleotide product analog (AADP+) molecule per enzyme chain. The corresponding covalently bound thioredoxin substrate molecules (one per enzyme monomer) are chains G and H (corresponding to thioredoxin chains D and C in the primary citation).

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Components

#1: Protein
THIOREDOXIN REDUCTASE


Mass: 34513.703 Da / Num. of mol.: 4 / Mutation: C135S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9P4, EC: 1.6.4.5
#2: Protein
THIOREDOXIN 1


Mass: 11671.322 Da / Num. of mol.: 4 / Mutation: C35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2
Details: Purchased from Sigma Chemical Company, St. Louis, MO
Comment: FAD*YM
#4: Chemical
ChemComp-3AA / 3-AMINOPYRIDINE-ADENINE DINUCLEOTIDE PHOSPHATE / ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) 2'-(DIHYDROGEN PHOSPHATE)ESTER WITH 3-(AMINO)-1-BETA-D-RIBOFURANOSYLPYRIDINIUM INNER SALT


Mass: 716.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H29N7O16P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: cacodylate, ammonium sulfate, PEG 3350, 3-aminopyridine adenine dinucleotide phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
26.7 mMHEPES1drop
327 mMAADP+1drop
40.1 Mcacodylate1reservoir
550 %satammonium sulfate1reservoir
624 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→31.38 Å / Num. all: 598907 / Num. obs: 45732 / % possible obs: 99.8 % / Observed criterion σ(I): 3.4 / Redundancy: 13.1 % / Biso Wilson estimate: 140.2 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 15
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4492 / % possible all: 99
Reflection
*PLUS
Num. measured all: 598907
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9refinement
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TRB, 2TRX

1trb

2trx


Resolution: 2.95→31.38 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2194524.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: several solvent-exposed regions of the thioredoxin chains cannot be modeled from the density. These regions are apparent from B factors >100 A2 or atom occupancies of 0.5. They include ...Details: several solvent-exposed regions of the thioredoxin chains cannot be modeled from the density. These regions are apparent from B factors >100 A2 or atom occupancies of 0.5. They include residues 1-20 in chains C,G; 1-22 in chains D,H; residues 61-62 and 81-85 in chains D,H and other side chains.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2747 6 %RANDOM
Rwork0.205 ---
all0.207 45732 --
obs0.207 45528 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.11 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1-11.16 Å20 Å24.93 Å2
2---3.21 Å20 Å2
3----7.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.95→31.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12980 0 396 236 13612
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.862.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2 / Weight position: 150

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)
11GROUP 1 CHAIN A RESTRAINED TO CHAIN E GROUP 2 CHAIN B RESTRAINED TO CHAIN F GROUP 3 CHAIN C RESTRAINED TO CHAIN G GROUP 4 CHAIN D RESTRAINED TO CHAIN H0.70.217
220.7970.11
330.4030.41
440.4270.198
LS refinement shellResolution: 2.95→3.06 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.369 272 6.1 %
Rwork0.323 4188 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAMS:PARAM_CNS.FADPARAMS:TOPH_CNS.FAD
X-RAY DIFFRACTION4PARAMS:PARAM_SHORT_CNS.AAPARAMS:TOPH_SHORT_CNS.AADP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 6 % / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.369 / % reflection Rfree: 6.1 % / Rfactor Rwork: 0.323

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