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- PDB-4hs1: High-resolution crystal structure of Glutaredoxin like protein Nr... -

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Basic information

Entry
Database: PDB / ID: 4hs1
TitleHigh-resolution crystal structure of Glutaredoxin like protein NrdH from Mycobacterium tuberculosis.
ComponentsGlutaredoxin NrdH, putative
KeywordsELECTRON TRANSPORT / Thioredoxin / Glutaredoxin like / Thioredoxin Reductase / Cytosol
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 / DI(HYDROXYETHYL)ETHER / Glutaredoxin-like protein NrdH
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.87 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
DepositionOct 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 20, 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)9,6146
Polymers9,2571
Non-polymers3585
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.595, 47.705, 26.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 9256.525 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 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95106

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.73 Å3/Da / Density % sol: 28.97 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Ammonium Nitrate, 20% PEG 3350, 10mM Tris, 50mM NaCl, 1% Glycerol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.71255 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2012
RadiationMonochromator: Band pass 1.9x10-4 for a Si(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71255 Å / Relative weight: 1
ReflectionResolution: 0.87→23.853 Å / Num. obs: 53538 / % possible obs: 99.8 % / Redundancy: 9.2 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID
0.87-0.926.50.941.976481
2.75-23.8512.60.03559.618821

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F2I

4f2i


Resolution: 0.87→23.853 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 15.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1436 1985 3.73 %RANDOM
Rwork0.1283 ---
obs0.1288 53208 99.32 %-
Solvent computationShrinkage radii: 1.4 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.87→23.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms630 0 22 98 750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023816
X-RAY DIFFRACTIONf_angle_d2.1771128
X-RAY DIFFRACTIONf_dihedral_angle_d14.651319
X-RAY DIFFRACTIONf_chiral_restr0.09129
X-RAY DIFFRACTIONf_plane_restr0.012147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.8701-0.89180.31271410.313353197
0.8918-0.91590.29531420.274353899
0.9159-0.94290.23381310.2258357599
0.9429-0.97330.21051490.195363199
0.9733-1.00810.20551270.1646361599
1.0081-1.04850.15651450.1324359999
1.0485-1.09620.15021420.11143638100
1.0962-1.1540.12991310.0963671100
1.154-1.22630.12251540.08933661100
1.2263-1.3210.11621420.08533678100
1.321-1.45390.10411440.0923697100
1.4539-1.66420.1091420.09653718100
1.6642-2.09650.1171450.11723744100
2.0965-23.86150.15111500.14143927100

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