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- PDB-3r5w: Structure of Ddn, the Deazaflavin-dependent nitroreductase from M... -

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Entry
Database: PDB / ID: 3r5w
TitleStructure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420
ComponentsDeazaflavin-dependent nitroreductase
KeywordsOXIDOREDUCTASE / PA-824 / OPC-67683 / nitroimidazoles / split barrel-like fold / DUF385 / deazaflavin-dependent nitroreductase / F420
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
COENZYME F420 / Deazaflavin-dependent nitroreductase / Deazaflavin-dependent nitroreductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.786 Å
AuthorsCellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I.M. / Choi, I. / Nayya, A. / Lee, Y.S. ...Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I.M. / Choi, I. / Nayya, 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 20, 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
Revision 1.3Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deazaflavin-dependent nitroreductase
B: Deazaflavin-dependent nitroreductase
C: Deazaflavin-dependent nitroreductase
D: Deazaflavin-dependent nitroreductase
E: Deazaflavin-dependent nitroreductase
K: Deazaflavin-dependent nitroreductase
L: Deazaflavin-dependent nitroreductase
M: Deazaflavin-dependent nitroreductase
N: Deazaflavin-dependent nitroreductase
O: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,30220
Polymers127,56610
Non-polymers7,73610
Water23,0591280
1
A: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
K: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
L: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
M: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
N: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
O: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers12,7571
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.336, 89.419, 127.678
Angle α, β, γ (deg.)90.000, 96.290, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein
Deazaflavin-dependent nitroreductase


Mass: 12756.584 Da / Num. of mol.: 10
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-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C29H36N5O18P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1280 / 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

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3.6 M Na-formate, 10% glycerol with equimolar protein and F420, pH 8.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.979
SYNCHROTRONALS 5.0.220.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJul 10, 2009
ADSC QUANTUM 315r2CCDJul 10, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal, cylindrically bent, Si(220)SINGLE WAVELENGTHMx-ray1
2Single crystal, cylindrically bent, Si(220)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21
ReflectionResolution: 1.786→50 Å / Num. all: 174250 / Num. obs: 174250 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.073 / Χ2: 1.826 / Net I/σ(I): 22.9
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.786-1.863.20.7221.6171500.9496.3
1.86-1.943.20.5252.79170601.4496.3
1.94-2.033.20.2714.607173711.00797.4
2.03-2.133.10.226.467173831.30897.5
2.13-2.273.10.1619.596173881.59897.6
2.27-2.443.10.11312.863175771.48398.4
2.44-2.693.10.09217.588175701.85998.4
2.69-3.0830.0725.689175872.41498.4
3.08-3.882.80.04838.687175143.18697.5
3.88-502.80.0445.667176503.49997.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.44 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.37 Å
Translation2.5 Å42.37 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3R5R (preliminary model)

3r5r


Resolution: 1.786→42.169 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.22 / σ(F): 0.08 / Phase error: 21.75 / Stereochemistry target values: CCP4 monomer library
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 7913 4.97 %random
Rwork0.1733 ---
obs0.175 159341 88.14 %-
all-159399 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.911 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 129.69 Å2 / Biso mean: 31.0082 Å2 / Biso min: 8.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.5771 Å20 Å2-2.9673 Å2
2--0.4187 Å2-0 Å2
3---0.1584 Å2
Refinement stepCycle: LAST / Resolution: 1.786→42.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8740 0 530 1280 10550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139560
X-RAY DIFFRACTIONf_angle_d1.56813090
X-RAY DIFFRACTIONf_chiral_restr0.1031439
X-RAY DIFFRACTIONf_plane_restr0.0081631
X-RAY DIFFRACTIONf_dihedral_angle_d22.0583590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.786-1.84930.26976120.241611016116281162865
1.8493-1.92340.31126760.257312800134761347675
1.9234-2.01090.24527560.200115116158721587288
2.0109-2.11690.23558290.19215343161721617289
2.1169-2.24950.22897430.190915457162001620090
2.2495-2.42320.22268160.177315553163691636991
2.4232-2.6670.22148850.184316025169101691094
2.667-3.05290.23468680.193216557174251742596
3.0529-3.84590.17948400.150616703175431754397
3.8459-42.18090.15868880.138116858177461774697
Refinement TLS params.Method: refined / Origin x: -17.6968 Å / Origin y: -17.8438 Å / Origin z: -31.9952 Å
111213212223313233
T0.0829 Å20.0011 Å20.0248 Å2-0.0898 Å20.0089 Å2--0.0504 Å2
L0.4069 °2-0.0099 °20.1453 °2-0.2797 °20.0284 °2--0.3389 °2
S-0.0117 Å °0.0138 Å °-0.0152 Å °-0.0063 Å °-0.0091 Å °0.0069 Å °-0.0076 Å °0.0242 Å °0.0182 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA43 - 151
2X-RAY DIFFRACTION1allB43 - 151
3X-RAY DIFFRACTION1allC43 - 151
4X-RAY DIFFRACTION1allD43 - 151
5X-RAY DIFFRACTION1allE43 - 151
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allA1
8X-RAY DIFFRACTION1allD1
9X-RAY DIFFRACTION1allB1
10X-RAY DIFFRACTION1allC1
11X-RAY DIFFRACTION1allK43 - 151
12X-RAY DIFFRACTION1allL43 - 151
13X-RAY DIFFRACTION1allM43 - 151
14X-RAY DIFFRACTION1allN43 - 151
15X-RAY DIFFRACTION1allO43 - 151
16X-RAY DIFFRACTION1allO1
17X-RAY DIFFRACTION1allK1
18X-RAY DIFFRACTION1allN1
19X-RAY DIFFRACTION1allL1
20X-RAY DIFFRACTION1allM1
21X-RAY DIFFRACTION1allL - C1 - 1280

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