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- PDB-4f2i: Crystal structure of glutaredoxin-like NrdH from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 4f2i
TitleCrystal structure of glutaredoxin-like NrdH from Mycobacterium tuberculosis
ComponentsGlutaredoxin NrdH, putative
KeywordsELECTRON TRANSPORT / THIOREDOXIN FOLD / NRDH / GLUTAREDOXIN / REDOX PROTEIN
Function / homology
Function and homology information


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
NITRATE ION / Glutaredoxin-like protein NrdH / Glutaredoxin-like protein NrdH
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsPhulera, S. / Mande, S.C.
CitationJournal: Biochemistry / Year: 2013
Title: The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87 A Suggests a Possible Mode of Its Activity.
Authors: Phulera, S. / Mande, S.C.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin NrdH, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2493
Polymers9,1251
Non-polymers1242
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.000, 48.180, 26.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

21A-277-

HOH

31A-279-

HOH

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Components

#1: Protein Glutaredoxin NrdH, putative / Glutaredoxin-like electron transporter nrdH / PROBABLE GLUTAREDOXIN ELECTRON TRANSPORT COMPONENT OF ...Glutaredoxin-like electron transporter nrdH / PROBABLE GLUTAREDOXIN ELECTRON TRANSPORT COMPONENT OF NRDEF (GLUTAREDOXIN-LIKE PROTEIN) NRDH


Mass: 9125.329 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: MT3139, nrdH, Rv3053c, TBSG_00920 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95106, UniProt: I6YB06*PLUS
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.8 Å3/Da / Density % sol: 31.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22% PEG 3350, 0.15M ammonium nitrate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 22, 2011 / Details: Bruker multilayer
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.67→35.34 Å / Num. all: 8023 / Num. obs: 8023 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.67-1.766.70.41541065192.3
5.27-35.345.70.03429.7304199.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXAutobuildmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXAutobuildphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R7H

1r7h


Resolution: 1.67→26.23 Å / SU ML: 0.27 / σ(F): 1.41 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 810 10.13 %RANDOM
Rwork0.1716 ---
all0.1757 7997 --
obs0.1757 7997 98.69 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.584 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0129 Å2-0 Å20 Å2
2---0.6614 Å20 Å2
3---0.6742 Å2
Refinement stepCycle: LAST / Resolution: 1.67→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms635 0 8 83 726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01674
X-RAY DIFFRACTIONf_angle_d1.16921
X-RAY DIFFRACTIONf_dihedral_angle_d13.817239
X-RAY DIFFRACTIONf_chiral_restr0.067105
X-RAY DIFFRACTIONf_plane_restr0.007118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.67-1.77460.38421280.3478114897
1.7746-1.91150.24071350.1867115298
1.9115-2.10380.18671290.1376119098
2.1038-2.40810.18741360.1376118599
2.4081-3.03320.19961400.16791215100
3.0332-26.23320.20971420.17061297100

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