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- PDB-4bn6: Nitroreductase CinD from Lactococcus lactis in complex with chlor... -

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Basic information

Entry
Database: PDB / ID: 4bn6
TitleNitroreductase CinD from Lactococcus lactis in complex with chloramphenicol
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
CHLORAMPHENICOL / FLAVIN MONONUCLEOTIDE / Nitroreductase domain-containing protein
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.462 Å
AuthorsOberholzer, A.E. / Baumgartner, R. / Waltersperger, S.
CitationJournal: To be Published
Title: Nitroreductase Cind from Lactococcus Lactis in Complex with Chloramphenicol
Authors: Oberholzer, A.E. / Baumgartner, R. / Waltersperger, S.
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)23,2113
Polymers22,4311
Non-polymers7792
Water4,810267
1
A: COPPER INDUCED NITROREDUCTASE D
hetero molecules

A: COPPER INDUCED NITROREDUCTASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4216
Polymers44,8622
Non-polymers1,5594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8840 Å2
ΔGint-63.7 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.020, 121.605, 68.689
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-2004-

HOH

21A-2078-

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
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Strain: IL1403 / Production host: ESCHERICHIA COLI DH5[ALPHA] (bacteria) / References: UniProt: Q9CED0
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CLM / CHLORAMPHENICOL / Chloramphenicol


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.52 Å3/Da / Density % sol: 51.21 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→100 Å / Num. obs: 38856 / % possible obs: 98.3 % / Observed criterion σ(I): 2.2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21
Reflection shellResolution: 1.46→1.55 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.2 / % possible all: 96.3

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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: 1.462→29.904 Å / SU ML: 0.13 / σ(F): 2 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1747 1943 5 %
Rwork0.1513 --
obs0.1525 38846 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 1.462→29.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 51 267 1801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041584
X-RAY DIFFRACTIONf_angle_d0.9432158
X-RAY DIFFRACTIONf_dihedral_angle_d14.766579
X-RAY DIFFRACTIONf_chiral_restr0.054234
X-RAY DIFFRACTIONf_plane_restr0.006277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.462-1.49850.2851320.26082500X-RAY DIFFRACTION94
1.4985-1.5390.25861360.22732596X-RAY DIFFRACTION98
1.539-1.58430.2411360.21172581X-RAY DIFFRACTION98
1.5843-1.63550.24021360.18792586X-RAY DIFFRACTION98
1.6355-1.69390.221370.17512596X-RAY DIFFRACTION98
1.6939-1.76170.16511380.15962627X-RAY DIFFRACTION99
1.7617-1.84190.1871380.15422622X-RAY DIFFRACTION98
1.8419-1.9390.1781390.1432633X-RAY DIFFRACTION99
1.939-2.06040.17131400.14242649X-RAY DIFFRACTION100
2.0604-2.21950.14111400.12562661X-RAY DIFFRACTION99
2.2195-2.44280.15581390.12982671X-RAY DIFFRACTION99
2.4428-2.7960.16481410.13862681X-RAY DIFFRACTION99
2.796-3.52180.15291430.14332716X-RAY DIFFRACTION99
3.5218-29.910.17471480.15252784X-RAY DIFFRACTION98
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)
14.4272-0.4326-1.38621.36421.60822.5467-0.0676-0.2017-0.1504-0.0002-0.0376-0.02230.05940.23260.13110.08950.0247-0.02380.08120.04130.1115-15.3618-29.862413.9511
23.2716-2.5927-2.59126.1983-0.30054.7209-0.05840.3895-0.5355-0.325-0.2161-0.04240.347-0.01740.17610.1076-0.00160.00090.1395-0.040.1116-25.1282-29.15972.4758
31.3373-0.4591-0.27122.008-0.40081.83930.00820.16780.3497-0.1229-0.0441-0.2329-0.25440.09740.01050.1501-0.0262-0.02290.08240.0220.1456-19.7817-13.10264.0477
41.0339-0.0352-0.22540.5080.04311.9875-0.00720.02680.1394-0.018-0.0056-0.0298-0.29070.02440.00420.0969-0.0129-0.01720.06370.00660.1187-21.2878-16.186913.164
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 115 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 116 THROUGH 202 )

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