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- PDB-1h75: Structural basis for the thioredoxin-like activity profile of the... -

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Basic information

Entry
Database: PDB / ID: 1h75
TitleStructural basis for the thioredoxin-like activity profile of the glutaredoxin-like protein NrdH-redoxin from Escherichia coli.
ComponentsGLUTAREDOXIN-LIKE PROTEIN NRDH
KeywordsELECTRON TRANSPORT / NRDH / THIOREDOXIN / GLUTAREDOXIN / REDOX PROTEIN
Function / homology
Function and homology information


positive regulation of oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis / electron transfer activity
Similarity search - Function
Glutaredoxin-like protein NrdH / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin-like protein NrdH / Glutaredoxin-like protein NrdH
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsStehr, M. / Schneider, G. / Aslund, F. / Holmgren, A. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structural Basis for the Thioredoxin-Like Activity Profile of the Glutaredoxin-Like Nrdh-Redoxin from Escherichia Coli
Authors: Stehr, M. / Schneider, G. / Aslund, F. / Holmgren, A. / Lindqvist, Y.
History
DepositionJul 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAREDOXIN-LIKE PROTEIN NRDH


Theoretical massNumber of molelcules
Total (without water)9,1521
Polymers9,1521
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.151, 41.346, 58.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTAREDOXIN-LIKE PROTEIN NRDH


Mass: 9152.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47414, UniProt: P0AC65*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growpH: 9.1 / Details: pH 9.10
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 MCHES1drop
216 mg/mlprotein1drop
31.20 Msodium citrate1reservoir
4200 mMTris-HCl1reservoir
55 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0292
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0292 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 8503 / % possible obs: 96.4 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 113655
Reflection shell
*PLUS
% possible obs: 88.7 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 897 0.106 %RANDOM
Rwork0.2 ---
obs0.2 8491 96.4 %-
Solvent computationBsol: 80.6 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.796 Å20 Å20 Å2
2--3.919 Å20 Å2
3---2.877 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms609 0 0 81 690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.31
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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