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- PDB-3r5p: Structure of Ddn, the Deazaflavin-dependent nitroreductase from M... -

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Basic information

Entry
Database: PDB / ID: 3r5p
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 19, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 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: Deazaflavin-dependent nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5573
Polymers13,3651
Non-polymers1922
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.176, 96.176, 33.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Deazaflavin-dependent nitroreductase


Mass: 13364.905 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.6M (NH4)2SO4, 0.1M Citric acid, pH 4.0, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2009
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 12.36 / Number: 82014 / Rmerge(I) obs: 0.116 / Χ2: 0.87 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 16598 / % possible obs: 90.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.755010010.041.2335.3
3.774.7510010.0521.55.3
3.293.7710010.0851.9515.3
2.993.2910010.0971.4675.5
2.782.9910010.1130.875.5
2.612.7810010.1350.7285.5
2.482.6110010.1540.6985.5
2.382.4810010.190.695.5
2.282.3810010.2420.675.5
2.22.2810010.2560.6765.5
2.142.210010.30.6455.5
2.072.1410010.340.6135.4
2.022.0710010.4040.5735.2
1.972.0299.810.4680.5594.7
1.931.9796.610.5060.5394.2
1.891.9389.310.5410.5473.7
1.851.8975.510.5930.5243.4
1.811.8563.210.8490.4663.1
1.781.8147.210.8260.4492.7
1.751.7837.210.4792.1
ReflectionResolution: 1.85→50 Å / Num. all: 15215 / Num. obs: 15215 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.113 / Χ2: 0.884 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.85-1.923.60.5721.21412380.51881.6
1.92-1.994.20.491.8815080.56396.8
1.99-2.085.10.4192.81815270.568100
2.08-2.195.50.3214.09515280.634100
2.19-2.335.50.2555.3515480.656100
2.33-2.515.50.1987.21115340.69100
2.51-2.765.50.14110.38915640.713100
2.76-3.165.50.10616.36815581.035100
3.16-3.995.40.08229.04315681.907100
3.99-505.30.04340.79216421.242100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.09 Å
Translation2.5 Å48.09 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 3R5L (preliminary model used for MR)

3r5l


Resolution: 1.85→41.645 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.22 / σ(F): 0.16 / Phase error: 19.06 / Stereochemistry target values: CCP4 monomer library
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 722 5.03 %random
Rwork0.1711 ---
obs0.1727 14350 92.36 %-
all-14356 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.477 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 82.33 Å2 / Biso mean: 24.6311 Å2 / Biso min: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.1752 Å2-0 Å2-0 Å2
2--3.1752 Å20 Å2
3----6.3505 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 10 108 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018961
X-RAY DIFFRACTIONf_angle_d1.7471315
X-RAY DIFFRACTIONf_chiral_restr0.136145
X-RAY DIFFRACTIONf_plane_restr0.009167
X-RAY DIFFRACTIONf_dihedral_angle_d18.227365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.85-1.99250.27521180.223621912309219175
1.9925-2.1930.22431600.174726462806264692
2.193-2.51030.21111530.165928252978282597
2.5103-3.16250.191400.162929273067292798
3.1625-41.6560.18311510.1656303931903039100

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