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- PDB-4k8m: High resolution structure of M.tb NRDH -

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Basic information

Entry
Database: PDB / ID: 4k8m
TitleHigh resolution structure of M.tb NRDH
ComponentsGlutaredoxin-like protein NrdH
KeywordsELECTRON TRANSPORT / THIOREDOXIN / REDOXIN / THIOREDOXIN REDUCTASE / RIBONUCLEOTIDE REDUCTASE
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 angstrom suggests a possible mode of its activity.
Authors: Phulera, S. / Mande, S.C.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Refinement description
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 9, 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-like protein NrdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4836
Polymers9,1251
Non-polymers3585
Water1,78399
1
A: Glutaredoxin-like protein NrdH
hetero molecules

A: Glutaredoxin-like protein NrdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,96612
Polymers18,2512
Non-polymers71510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2950 Å2
ΔGint-24 kcal/mol
Surface area10720 Å2
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-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: Rv3053c, RVBD_3053c / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: I6YB06

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Non-polymers , 5 types, 104 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.: 99 / 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: 1.76 Å3/Da / Density % sol: 29.98 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.71255 Å
DetectorType: MARCCD 225X225 / Detector: CCD / Date: Jul 27, 2012 / Details: MIRRORS
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→23.85 Å / Num. all: 53538 / Num. obs: 53538 / % possible obs: 99.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 9.2 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.4

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Processing

Software
NameClassification
MxCuBEdata collection
SOLVEphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F2I

4f2i


Resolution: 0.87→23.85 Å / σ(F): 1.35
RfactorNum. reflection% reflection
Rfree0.1553 1985 -
Rwork0.1402 --
obs-53208 99.32 %
Refinement stepCycle: LAST / Resolution: 0.87→23.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms630 0 22 99 751

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