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- PDB-1nec: NITROREDUCTASE FROM ENTEROBACTER CLOACAE -

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Basic information

Entry
Database: PDB / ID: 1nec
TitleNITROREDUCTASE FROM ENTEROBACTER CLOACAE
ComponentsPROTEIN (NITROREDUCTASE)
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / FMN
Function / homology
Function and homology information


2,4,6-trinitrotoluene catabolic process / Oxidoreductases / oxidoreductase activity / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHecht, H.J. / Bryant, C. / Erdmann, H. / Pelletier, H. / Sawaya, R.
Citation
Journal: To be Published
Title: Crystal Structure of Nitroreductase from Enterobacter Cloacae
Authors: Hecht, H.J. / Bryant, C. / Erdmann, H. / Pelletier, H. / Sawaya, R.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Purification and Characterization of an Oxygen-Insensitive Nad(P)Hrt Nitroreductase from Enterobacter Cloacae
Authors: Bryant, C. / Deluca, M.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Cloning, Nucleotide Sequence, and Expression of the Nitroreductase Gene from Enterobacter Cloacae
Authors: Bryant, C. / Hubbard, L. / Mcelroy, W.D.
History
DepositionMar 30, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 31, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: PROTEIN (NITROREDUCTASE)
B: PROTEIN (NITROREDUCTASE)
C: PROTEIN (NITROREDUCTASE)
D: PROTEIN (NITROREDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2298
Polymers95,4044
Non-polymers1,8254
Water5,765320
1
A: PROTEIN (NITROREDUCTASE)
B: PROTEIN (NITROREDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6154
Polymers47,7022
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (NITROREDUCTASE)
D: PROTEIN (NITROREDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6154
Polymers47,7022
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.000, 92.500, 102.500
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.88576, -0.38492, -0.25937), (-0.38654, -0.92108, 0.04689), (-0.25695, 0.05872, -0.96464)5.61466, -2.79669, 45.07178
2given(0.99981, 0.01889, 0.00409), (-0.01886, 0.9998, -0.00731), (-0.00423, 0.00723, 0.99996)21.20599, 46.84999, 6.01139
3given(0.87479, -0.40622, -0.26404), (-0.40621, -0.91198, 0.05726), (-0.26406, 0.05717, -0.96281)26.98569, 43.63158, 51.04205

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Components

#1: Protein
PROTEIN (NITROREDUCTASE)


Mass: 23850.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: ATCC 43560 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01234
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET 1 HAS BEEN CLEAVED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43 %
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 52520 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062
Reflection shellHighest resolution: 2.1 Å / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NOX

1nox


Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 108-131 ARE DISORDERED IN CHAIN A AND CHAIN C
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2359 5 %RANDOM
Rwork0.18 ---
obs0.17 44552 95 %-
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 124 320 7152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6252
X-RAY DIFFRACTIONp_mcangle_it2.4013
X-RAY DIFFRACTIONp_scbond_it2.0022
X-RAY DIFFRACTIONp_scangle_it3.0833
X-RAY DIFFRACTIONp_plane_restr0.0280.03
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.2791
X-RAY DIFFRACTIONp_multtor_nbd0.2281
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1451
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor15.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.820
X-RAY DIFFRACTIONp_special_tor

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