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- PDB-7a9a: Crystal structure of rubredoxin B (Rv3250c) from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 7a9a
TitleCrystal structure of rubredoxin B (Rv3250c) from Mycobacterium tuberculosis
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / IRON SULFUR / METALLOPROTEIN / CYTOCHROME P450 REDOX PARTNER / CYP / CYP124 / CYP125 / CYP142
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Rubredoxin
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsVakhrameev, D. / Kavaleuski, A. / Bukhdruker, S. / Marin, E. / Sushko, T. / Grabovec, I.P. / Gilep, A. / Strushkevich, N. / Borshchevskiy, V.
Funding support Russian Federation, Belarus, 2items
OrganizationGrant numberCountry
Russian Foundation for Basic Research20-54-00005 Russian Federation
Belarusian Republican Foundation for Fundamental ResearchB20R-061Belarus
CitationJournal: Bioorg.Chem. / Year: 2021
Title: A new twist of rubredoxin function in M. tuberculosis.
Authors: Sushko, T. / Kavaleuski, A. / Grabovec, I. / Kavaleuskaya, A. / Vakhrameev, D. / Bukhdruker, S. / Marin, E. / Kuzikov, A. / Masamrekh, R. / Shumyantseva, V. / Tsumoto, K. / Borshchevskiy, V. ...Authors: Sushko, T. / Kavaleuski, A. / Grabovec, I. / Kavaleuskaya, A. / Vakhrameev, D. / Bukhdruker, S. / Marin, E. / Kuzikov, A. / Masamrekh, R. / Shumyantseva, V. / Tsumoto, K. / Borshchevskiy, V. / Gilep, A. / Strushkevich, N.
History
DepositionSep 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubredoxin
B: Rubredoxin
C: Rubredoxin
D: Rubredoxin
E: Rubredoxin
F: Rubredoxin
G: Rubredoxin
H: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,49768
Polymers54,4208
Non-polymers4,07860
Water10,431579
1
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1827
Polymers6,8021
Non-polymers3806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2478
Polymers6,8021
Non-polymers4457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,37810
Polymers6,8021
Non-polymers5769
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3579
Polymers6,8021
Non-polymers5548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2267
Polymers6,8021
Non-polymers4246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,43510
Polymers6,8021
Non-polymers6329
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3549
Polymers6,8021
Non-polymers5518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3188
Polymers6,8021
Non-polymers5167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.035, 61.322, 76.910
Angle α, β, γ (deg.)90.152, 90.319, 93.754
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Rubredoxin /


Mass: 6802.464 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rubB, Rv3250c / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6YFL7

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Non-polymers , 7 types, 639 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Fe
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.82 Å3/Da / Density % sol: 32.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM Tris-HCl, 50 mM zinc acetate, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.17→47.95 Å / Num. obs: 119411 / % possible obs: 93.18 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.13 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.086 / Rrim(I) all: 0.16 / Net I/σ(I): 4.69
Reflection shellResolution: 1.17→1.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 2.077 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 119411 / CC1/2: 0.295 / Rpim(I) all: 1.312 / Rrim(I) all: 2.466 / % possible all: 90.95

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
REFMAC5.8.0258refinement
MoRDaphasing
STARANISOdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PYA

2pya


Resolution: 1.17→47.95 Å / SU ML: 0.1186 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 23.9895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 3786 4.95 %
Rwork0.1537 72647 -
obs0.1554 76433 59.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.47 Å2
Refinement stepCycle: LAST / Resolution: 1.17→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 113 579 4408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434230
X-RAY DIFFRACTIONf_angle_d0.65725804
X-RAY DIFFRACTIONf_chiral_restr0.0729555
X-RAY DIFFRACTIONf_plane_restr0.0055786
X-RAY DIFFRACTIONf_dihedral_angle_d15.56721624
LS refinement shellResolution: 1.17→47.95 Å

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