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- PDB-2wqf: Crystal Structure of the Nitroreductase CinD from Lactococcus lac... -

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Basic information

Entry
Database: PDB / ID: 2wqf
TitleCrystal Structure of the Nitroreductase CinD from Lactococcus lactis in Complex with FMN
ComponentsCOPPER INDUCED NITROREDUCTASE D
KeywordsOXIDOREDUCTASE / NITROREDUCTASE / COPR REGULATED PROTEIN
Function / homology
Function and homology information


cellular response to oxidative stress / oxidoreductase activity / nucleotide binding / cytoplasm
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 / Nitroreductase domain-containing protein
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWaltersperger, S.M. / Oberholzer, A.E. / Solioz, M. / Baumann, U.
CitationJournal: J.Bacteriol. / Year: 2010
Title: Structure and Function of Cind (Ytjd) of Lactococcus Lactis, a Copper-Induced Nitroreductase Involved in Defense Against Oxidative Stress.
Authors: Mermod, M. / Mourlane, F. / Waltersperger, S. / Oberholzer, A.E. / Baumann, U. / Solioz, M.
History
DepositionAug 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)23,0192
Polymers22,5621
Non-polymers4561
Water5,332296
1
A: COPPER INDUCED NITROREDUCTASE D
hetero molecules

A: COPPER INDUCED NITROREDUCTASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0384
Polymers45,1252
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7470 Å2
ΔGint-43.2 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.843, 120.147, 68.659
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-2154-

HOH

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Components

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


Mass: 22562.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Strain: IL1403 / Plasmid: PPROEX HTA / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.2 % / Description: NONE
Crystal growDetails: 0.2M MGCL2, 0.1M TRISHCL PH 8.0, 5% MPD (V/V), 20% PEG 3350 (W/V), 1MM FMN, 4MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→49.15 Å / Num. obs: 48865 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.36
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3

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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 2IFA

2ifa


Resolution: 1.35→32.134 Å / SU ML: 0 / σ(F): 2 / Phase error: 14.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1555 1466 3 %
Rwork0.1315 --
obs0.1322 48850 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.023 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0209 Å20 Å20 Å2
2---0.198 Å2-0 Å2
3---0.2188 Å2
Refinement stepCycle: LAST / Resolution: 1.35→32.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 31 296 1796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073041
X-RAY DIFFRACTIONf_angle_d0.8635489
X-RAY DIFFRACTIONf_dihedral_angle_d15.589756
X-RAY DIFFRACTIONf_chiral_restr0.069234
X-RAY DIFFRACTIONf_plane_restr0.005475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.39830.24241420.19464594X-RAY DIFFRACTION97
1.3983-1.45420.23361430.17124639X-RAY DIFFRACTION98
1.4542-1.52040.2091440.14524641X-RAY DIFFRACTION98
1.5204-1.60060.15821450.11874685X-RAY DIFFRACTION99
1.6006-1.70090.15391460.10144735X-RAY DIFFRACTION100
1.7009-1.83220.15541470.10574744X-RAY DIFFRACTION100
1.8322-2.01650.15441470.11234756X-RAY DIFFRACTION100
2.0165-2.30830.14471480.11274797X-RAY DIFFRACTION100
2.3083-2.90790.15431490.11934822X-RAY DIFFRACTION100
2.9079-32.14350.13331550.14814971X-RAY DIFFRACTION99

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