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- PDB-4bn9: Nitroreductase CinD from Lactococcus lactis in complex with nicot... -

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Basic information

Entry
Database: PDB / ID: 4bn9
TitleNitroreductase CinD from Lactococcus lactis in complex with nicotinic acid
ComponentsCOPPER INDUCED NITROREDUCTASE D
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


: / cellular response to oxidative stress / 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 / NICOTINIC ACID / Nitroreductase domain-containing protein
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.084 Å
AuthorsBaumgartner, R. / Waltersperger, S. / Oberholzer, A.E.
CitationJournal: To be Published
Title: Nitroreductase Cind from Lactococcus Lactis
Authors: Baumgartner, R. / Waltersperger, S. / 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

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Assembly

Deposited unit
A: COPPER INDUCED NITROREDUCTASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0113
Polymers22,4311
Non-polymers5792
Water1,874104
1
A: COPPER INDUCED NITROREDUCTASE D
hetero molecules

A: COPPER INDUCED NITROREDUCTASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0216
Polymers44,8622
Non-polymers1,1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8280 Å2
ΔGint-30.7 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.811, 122.626, 68.819
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-2003-

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 NICOTINIC ACID
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-NIO / NICOTINIC ACID / Niacin


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 51.52 % / 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: 2.08→100 Å / Num. obs: 13766 / % possible obs: 98.5 % / Observed criterion σ(I): 3.7 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.92
Reflection shellResolution: 2.08→2.21 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.75 / % possible all: 97

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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
Resolution: 2.084→40.064 Å / SU ML: 0.22 / σ(F): 2.01 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2027 688 5 %
Rwork0.1755 --
obs0.1769 13739 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52 Å2
Refinement stepCycle: LAST / Resolution: 2.084→40.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 40 104 1640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031588
X-RAY DIFFRACTIONf_angle_d0.6882161
X-RAY DIFFRACTIONf_dihedral_angle_d15.318582
X-RAY DIFFRACTIONf_chiral_restr0.044233
X-RAY DIFFRACTIONf_plane_restr0.002279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0842-2.24510.26651330.23152516X-RAY DIFFRACTION97
2.2451-2.4710.22661360.19482578X-RAY DIFFRACTION99
2.471-2.82840.21511360.18362595X-RAY DIFFRACTION99
2.8284-3.56320.21111390.17912628X-RAY DIFFRACTION99
3.5632-40.07160.17651440.15562734X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.9191-0.2492-1.05461.13041.67132.9151-0.19410.0508-0.12090.00670.0345-0.1086-0.02830.60110.16510.3258-0.0174-0.04440.58180.05280.3517-15.3406-30.225313.8198
26.4512-0.4477-2.66543.11290.09333.9873-0.13830.58160.0337-0.497-0.153-0.1441-0.37430.17470.19340.3759-0.0403-0.08790.49160.07790.2313-23.093-21.84332.3775
32.501-1.3103-0.79793.215-1.95443.0762-0.23130.29770.67310.43220.1493-1.2913-1.10350.73940.13870.7701-0.2606-0.05420.8220.15030.7055-4.3171-11.78134.1346
42.4284-0.1443-0.34480.81910.29243.4148-0.06760.09020.5278-0.1203-0.0557-0.0753-0.70090.11630.11810.4596-0.0599-0.08350.38520.02120.4192-23.1898-15.328611.7243
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 62 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 63 THROUGH 96 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 97 THROUGH 202 )

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