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- PDB-3r5z: Structure of a Deazaflavin-dependent reductase from Nocardia farc... -

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Basic information

Entry
Database: PDB / ID: 3r5z
TitleStructure of a Deazaflavin-dependent reductase from Nocardia farcinica, with co-factor F420
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / split barrel-like fold / DUF385 / deazaflavin-dependent reductase / F420-dependent reductase / FDR / F420
Function / homology
Function and homology information


oxidoreductase activity
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 / Uncharacterized protein
Similarity search - Component
Biological speciesNocardia farcinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.503 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: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3085
Polymers32,6652
Non-polymers1,6433
Water4,342241
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1062
Polymers16,3321
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2023
Polymers16,3321
Non-polymers8702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.704, 56.939, 66.003
Angle α, β, γ (deg.)90.000, 105.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein


Mass: 16332.296 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica (bacteria) / Gene: NFA_18080 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / References: UniProt: Q5YYT7
#2: Chemical ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H36N5O18P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 2000, 0.1M acetate, 0.2M (NH4)2SO4 with equimolar protein and co-factor, pH 4.6, 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: Oct 28, 2009
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 42118 / Num. obs: 42118 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Χ2: 2.198 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.5-1.551.80.4731.55936480.86782.1
1.55-1.6220.4361.86939980.93489
1.62-1.692.20.3762.5442031.18593.5
1.69-1.782.40.3513.38343012.22696
1.78-1.892.50.2625.43243842.06297.2
1.89-2.042.60.1679.70543802.10297.7
2.04-2.242.60.11814.97443752.45897.3
2.24-2.562.50.09519.70543352.73696
2.56-3.232.40.06527.72442183.2893.1
3.23-502.30.03637.80342762.94792.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.77 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.42 Å
Translation2.5 Å42.42 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 3R5Y

3r5y


Resolution: 1.503→37.515 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8802 / SU ML: 0.18 / σ(F): 0.05 / Phase error: 19.4 / Stereochemistry target values: CCP4 monomer library
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1967 5.05 %random
Rwork0.1662 ---
obs0.1675 38957 86.2 %-
all-38975 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.589 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 85.36 Å2 / Biso mean: 21.3403 Å2 / Biso min: 4.71 Å2
Baniso -1Baniso -2Baniso -3
1-5.1172 Å2-0 Å21.8438 Å2
2---1.3982 Å20 Å2
3----3.719 Å2
Refinement stepCycle: LAST / Resolution: 1.503→37.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 111 241 2588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132442
X-RAY DIFFRACTIONf_angle_d1.493346
X-RAY DIFFRACTIONf_chiral_restr0.1354
X-RAY DIFFRACTIONf_plane_restr0.009423
X-RAY DIFFRACTIONf_dihedral_angle_d19.733896
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 (%)
1.503-1.55670.25731660.242327732939293966
1.5567-1.61910.28031760.212732073383338376
1.6191-1.69270.21211710.191834993670367081
1.6927-1.7820.25591950.180936123807380784
1.782-1.89360.19561860.166937883974397488
1.8936-2.03980.18642130.154739894202420293
2.0398-2.24510.18572180.149440354253425394
2.2451-2.56990.19072100.15840584268426894
2.5699-3.23750.18622150.163639814196419692
3.2375-37.52630.16382170.153740484265426592
Refinement TLS params.Method: refined / Origin x: 13.1895 Å / Origin y: 16.0503 Å / Origin z: 14.6961 Å
111213212223313233
T0.0031 Å20.0076 Å2-0.0038 Å2-0.0127 Å2-0.0056 Å2--0.0041 Å2
L0.3461 °20.0102 °2-0.0899 °2-0.6008 °2-0.2864 °2--0.8322 °2
S-0.0162 Å °-0.0283 Å °0.0165 Å °0.0204 Å °0.007 Å °0.017 Å °0.0119 Å °-0.0206 Å °0.0087 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 144
2X-RAY DIFFRACTION1allB5 - 144
3X-RAY DIFFRACTION1allB1 - 145
4X-RAY DIFFRACTION1allA1 - 145
5X-RAY DIFFRACTION1allB1 - 146
6X-RAY DIFFRACTION1allA - B1 - 241

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