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- PDB-4bn7: Nitroreductase CinD from Lactococcus lactis in complex with 2,6- ... -

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Basic information

Entry
Database: PDB / ID: 4bn7
TitleNitroreductase CinD from Lactococcus lactis in complex with 2,6- dichlorophenolindophenol
ComponentsCOPPER INDUCED NITROREDUCTASE D
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


cellular response to oxidative stress / oxidoreductase activity / nucleotide binding
Similarity search - Function
Nitroreductase Frm2/Hbn1-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-RLM / Nitroreductase domain-containing protein
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.723 Å
AuthorsWaltersperger, S. / Baumgartner, R. / Oberholzer, A.E.
CitationJournal: To be Published
Title: Nitroreductase Cind from Lactococcus Lactis
Authors: Waltersperger, S. / Baumgartner, R. / Oberholzer, A.E.
History
DepositionMay 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: COPPER INDUCED NITROREDUCTASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1583
Polymers22,4311
Non-polymers7262
Water4,143230
1
A: COPPER INDUCED NITROREDUCTASE D
hetero molecules

A: COPPER INDUCED NITROREDUCTASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3156
Polymers44,8622
Non-polymers1,4534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8050 Å2
ΔGint-45.8 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.109, 121.944, 68.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2146-

HOH

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Components

#1: Protein COPPER INDUCED NITROREDUCTASE D / PUTATIVE UNCHARACTERIZED PROTEIN YTJD


Mass: 22431.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: - FLAVIN MONONUCLEOTIDE COFACTOR - IN COMPLEX WITH 2,6-DICHLOROPHENOLINDOPHENOL
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Strain: IL1403 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / References: UniProt: Q9CED0
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-RLM / 2,6-bis(chloranyl)-4-[(4-hydroxyphenyl)amino]phenol


Mass: 270.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9Cl2NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.54 Å3/Da / Density % sol: 51.57 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→100 Å / Num. obs: 24444 / % possible obs: 99.8 % / Observed criterion σ(I): 2.2 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 1.72→1.83 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.25 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WQF

2wqf


Resolution: 1.723→49.459 Å / SU ML: 0.15 / σ(F): 2 / Phase error: 16.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1776 1223 5 %
Rwork0.1529 --
obs0.1542 24434 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.723→49.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 48 230 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051580
X-RAY DIFFRACTIONf_angle_d0.9832150
X-RAY DIFFRACTIONf_dihedral_angle_d15.856575
X-RAY DIFFRACTIONf_chiral_restr0.056230
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7231-1.79210.26751320.23182513X-RAY DIFFRACTION100
1.7921-1.87370.25861340.2022551X-RAY DIFFRACTION100
1.8737-1.97250.19641350.17942552X-RAY DIFFRACTION100
1.9725-2.09610.19291340.15142552X-RAY DIFFRACTION100
2.0961-2.25790.14381350.13672554X-RAY DIFFRACTION100
2.2579-2.48510.18211350.13612572X-RAY DIFFRACTION100
2.4851-2.84470.17541370.14172593X-RAY DIFFRACTION100
2.8447-3.58390.16111370.14172604X-RAY DIFFRACTION100
3.5839-49.47910.1641440.15182720X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3861-0.3321.37621.3445-1.5592.3243-0.0036-0.25480.0429-0.0024-0.01280.0282-0.0899-0.24440.05590.13660.03450.03060.0571-0.03590.1045-11.704229.97114.0707
23.5162-1.48342.07613.88850.03633.8609-0.04260.49270.5566-0.2161-0.1551-0.0009-0.3340.11070.12930.1479-0.00140.00660.12410.04040.1207-2.020529.38582.5182
34.08773.6368-0.69675.34891.89925.9841-0.1227-0.0349-0.31650.08260.0573-0.13490.36820.24030.0410.07830.0150.02160.08350.00960.08759.083317.93059.589
41.64590.6451-1.21541.688-0.19081.34730.14060.4516-0.2685-0.3702-0.06790.340.2033-0.2812-0.04820.2142-0.0144-0.0520.1603-0.04990.1598-13.44117.3795-1.4123
53.12070.5757-0.01993.28580.63643.618-0.18410.0187-0.67670.14760.12950.82390.5365-0.5269-0.0580.2106-0.06510.00550.2897-0.0410.4284-22.406411.18154.465
64.3745-3.65411.02924.6803-0.68372.76370.06310.2733-0.3314-0.0639-0.1039-0.240.43850.47040.00430.18220.02460.02570.1357-0.02170.20994.55169.09715.6712
73.338-1.01350.28423.35420.10462.3446-0.0162-0.1503-0.19020.02480.0229-0.16730.29450.16380.00810.1145-0.00260.01590.08480.00930.0717-0.665917.037813.3678
82.37360.8467-0.23123.2187-1.29486.17960.00240.3955-0.512-0.2444-0.09010.26290.5633-0.1630.03480.247-0.0318-0.03310.1713-0.09520.2886-11.89277.44412.1321
91.2924-0.18420.70140.6434-0.37712.0842-0.0425-0.0401-0.1006-0.00710.03870.05550.0764-0.12910.02990.0865-0.03170.02470.06060.01420.1217-8.210118.709216.9424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 22 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 23 THROUGH 35 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 36 THROUGH 45 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 46 THROUGH 62 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 63 THROUGH 96 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 97 THROUGH 115 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 116 THROUGH 151 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 152 THROUGH 164 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 165 THROUGH 202 )

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