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- PDB-4bnb: Nitroreductase CinD from Lactococcus lactis in complex with 4- ni... -

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Basic information

Entry
Database: PDB / ID: 4bnb
TitleNitroreductase CinD from Lactococcus lactis in complex with 4- nitroquinoline 1-oxide
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 / 4-NITROQUINOLINE 1-OXIDE / Nitroreductase domain-containing protein
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.478 Å
AuthorsWaltersperger, S. / Oberholzer, A.E. / Baumgartner, R.
CitationJournal: To be Published
Title: Nitroreductase Cind from Lactococcus Lactis in Complex with 2 4-Nitroquinoline 1-Oxidenone
Authors: Waltersperger, S. / Oberholzer, A.E. / Baumgartner, R.
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

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Assembly

Deposited unit
A: COPPER INDUCED NITROREDUCTASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2684
Polymers22,4311
Non-polymers8373
Water4,720262
1
A: COPPER INDUCED NITROREDUCTASE D
hetero molecules

A: COPPER INDUCED NITROREDUCTASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5368
Polymers44,8622
Non-polymers1,6736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8160 Å2
ΔGint-43.5 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.052, 120.518, 68.444
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-2002-

HOH

21A-2069-

HOH

31A-2142-

HOH

41A-2169-

HOH

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Components

#1: Protein COPPER INDUCED NITROREDUCTASE D


Mass: 22431.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: - FLAVIN MONONUCLEOTIDE COFACTOR - IN COMPLEX WITH 2 4-NITROPHENOL
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-YHX / 4-NITROQUINOLINE 1-OXIDE


Mass: 190.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.47 Å3/Da / Density % sol: 50.21 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→100 Å / Num. obs: 37568 / % possible obs: 99.2 % / Observed criterion σ(I): 2.9 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19
Reflection shellResolution: 1.48→1.57 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.9 / % possible all: 99.3

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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: 1.478→40.013 Å / SU ML: 0.14 / σ(F): 2 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1647 1879 5 %
Rwork0.1351 --
obs0.1366 37559 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.478→40.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 59 262 1811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031589
X-RAY DIFFRACTIONf_angle_d0.782160
X-RAY DIFFRACTIONf_dihedral_angle_d13.115578
X-RAY DIFFRACTIONf_chiral_restr0.048229
X-RAY DIFFRACTIONf_plane_restr0.004275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4776-1.51750.24641410.16712696X-RAY DIFFRACTION99
1.5175-1.56220.22131440.14742724X-RAY DIFFRACTION100
1.5622-1.61260.21211450.13782747X-RAY DIFFRACTION100
1.6126-1.67020.20491430.12642724X-RAY DIFFRACTION100
1.6702-1.73710.1761430.12552728X-RAY DIFFRACTION100
1.7371-1.81620.18791440.12532720X-RAY DIFFRACTION100
1.8162-1.91190.18261440.12512733X-RAY DIFFRACTION100
1.9119-2.03170.17531430.12172726X-RAY DIFFRACTION99
2.0317-2.18850.16371440.11682731X-RAY DIFFRACTION99
2.1885-2.40880.16031440.12132731X-RAY DIFFRACTION99
2.4088-2.75720.17221450.12822753X-RAY DIFFRACTION99
2.7572-3.47350.13271470.1342790X-RAY DIFFRACTION99
3.4735-40.02780.14951520.15462877X-RAY DIFFRACTION98

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