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- PDB-3r5l: Structure of Ddn, the Deazaflavin-dependent nitroreductase from M... -

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Basic information

Entry
Database: PDB / ID: 3r5l
TitleStructure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824
ComponentsDeazaflavin-dependent nitroreductase
KeywordsOXIDOREDUCTASE / PA-824 / split barrel-like fold / DUF385 / Deazaflavin-dependent nitroreductase / nitroimidazoles
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With other, known, physiological acceptors / coenzyme F420 binding / Oxidoreductases / peptidoglycan-based cell wall / oxidoreductase activity / plasma membrane
Similarity search - Function
F420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
Deazaflavin-dependent nitroreductase / Deazaflavin-dependent nitroreductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsCellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I.M. / Choi, I. / Nayyar, A. / Lee, Y.S. ...Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I.M. / Choi, I. / Nayyar, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. / Manjunatha, U.H. / Barry, C.E. / Spraggon, G. / Geierstanger, B.H.
CitationJournal: Structure / Year: 2012
Title: Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824.
Authors: Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I. / Choi, I. / Nayyar, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. ...Authors: Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I. / Choi, I. / Nayyar, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. / Manjunatha, U.H. / Barry, C.E. / Spraggon, G. / Geierstanger, B.H.
History
DepositionMar 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0042
Polymers13,8081
Non-polymers1951
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.167, 71.045, 50.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-386-

HOH

31A-401-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Deazaflavin-dependent nitroreductase


Mass: 13808.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ddn, MT3651, Rv3547 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli)
References: UniProt: P71854, UniProt: P9WP15*PLUS, Oxidoreductases
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1843.65
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop630% PEG 6000, 1M LiCl, 0.1 M MES, pH 6.0, vapor diffusion, sitting drop, temperature 277K
2772vapor diffusion, sitting drop630% PEG 6000, 0.1 M MES, pH 6.0, vapor diffusion, sitting drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.979
SYNCHROTRONALS 5.0.220.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDApr 4, 2009
ADSC QUANTUM 315r2CCDApr 4, 2009
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Double-crystal, Si(111)SINGLE WAVELENGTHx-ray1
2Double-crystal, Si(111)SINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 17466 / Num. obs: 17466 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.098 / Χ2: 3.302 / Net I/σ(I): 27.5
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.55-1.613.30.6262.517354.24899.5
1.61-1.6740.5313.29617771.32699.7
1.67-1.754.20.4334.87417571.61799.5
1.75-1.844.20.3127.62317381.89799.3
1.84-1.954.20.23411.32817562.4898.3
1.95-2.14.10.17416.4417223.12297.7
2.1-2.323.90.13621.9717144.0296.2
2.32-2.653.80.11427.72117205.08596.3
2.65-3.343.60.08336.74617385.47295.5
3.34-503.80.05848.6418094.84995.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.55→35.523 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.18 / σ(F): 0.03 / Phase error: 21.51 / Stereochemistry target values: CCP4 monomer library
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 866 5.21 %random
Rwork0.1799 ---
obs0.1815 16624 92.66 %-
all-16640 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.972 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 184.29 Å2 / Biso mean: 24.6062 Å2 / Biso min: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1-5.3241 Å2-0 Å2-0 Å2
2---4.0708 Å20 Å2
3----1.2532 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 12 120 1053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015980
X-RAY DIFFRACTIONf_angle_d1.7341339
X-RAY DIFFRACTIONf_chiral_restr0.126147
X-RAY DIFFRACTIONf_plane_restr0.01171
X-RAY DIFFRACTIONf_dihedral_angle_d20.837373
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.55-1.64680.33341370.265423512488248884
1.6468-1.77390.2141370.195825202657265790
1.7739-1.95240.20681400.169326492789278994
1.9524-2.23490.16881310.171527212852285296
2.2349-2.81560.24091620.174827112873287396
2.8156-35.53180.1921590.171528062965296595
Refinement TLS params.Method: refined / Origin x: 18.5547 Å / Origin y: -9.7374 Å / Origin z: -11.8571 Å
111213212223313233
T0.1574 Å20 Å20.0018 Å2-0.0981 Å2-0 Å2--0.0754 Å2
L0.3522 °20.0334 °20.1171 °2-0.7766 °20.5135 °2--0.8995 °2
S-0.0329 Å °0.0243 Å °-0.0151 Å °0.0028 Å °-0.0132 Å °-0.0209 Å °0.064 Å °-0.0368 Å °0.037 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA36 - 151
2X-RAY DIFFRACTION1allA1
3X-RAY DIFFRACTION1allA1 - 243

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