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- PDB-1kqd: Structure of Nitroreductase from E. cloacae Bound with 2e-Reduced... -

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Basic information

Entry
Database: PDB / ID: 1kqd
TitleStructure of Nitroreductase from E. cloacae Bound with 2e-Reduced Flavin Mononucleotide (FMN)
ComponentsOXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
KeywordsOXIDOREDUCTASE / nitroreductase / reduced hydroquinone / flavin
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: 1.9 Å
AuthorsHaynes, C.A. / Koder, R.L. / Miller, A.F. / Rodgers, D.W.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structures of nitroreductase in three states: effects of inhibitor binding and reduction.
Authors: Haynes, C.A. / Koder, R.L. / Miller, A.F. / Rodgers, D.W.
History
DepositionJan 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
B: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
C: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
D: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7548
Polymers95,9294
Non-polymers1,8254
Water7,873437
1
A: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
B: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8774
Polymers47,9642
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-49 kcal/mol
Surface area16910 Å2
MethodPISA
2
C: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
D: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8774
Polymers47,9642
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-47 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.830, 79.980, 97.250
Angle α, β, γ (deg.)90.00, 93.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimer. Chains A and B represent one dimer, chains C and D represent the other dimer; both dimers are in the asymmetric unit. We are depositing all four monomers.

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Components

#1: Protein
OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE


Mass: 23982.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Plasmid: pET24d(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01234, EC: 1.6.6.-
#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.: 437 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: homopipes, acetate, PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.75 mg/mlprotein1drop
210 mMHEPES1droppH7.
350 mM1dropKCl
4100 mg/mlhomopipes1reservoirpH4.8
525 mMacetate1reservoir
615 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 25, 2000 / Details: graded multi-layer
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 63677 / Num. obs: 62505 / % possible obs: 0.982 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.6
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 7.5 / % possible all: 0.889
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 97.7 % / Redundancy: 4 %
Reflection shell
*PLUS
% possible obs: 88.9 %

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6321 10.11 %RANDOM
Rwork0.185 ---
all0.195 63677 --
obs0.195 62505 --
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 124 437 7269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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