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- PDB-3x21: Crystal structure of Escherichia coli nitroreductase NfsB mutant ... -

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Basic information

Entry
Database: PDB / ID: 3x21
TitleCrystal structure of Escherichia coli nitroreductase NfsB mutant T41L/N71S/F124W
ComponentsOxygen-insensitive NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Nitroreductase / regioselectivity / dinitrocompounds
Function / homology
Function and homology information


oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 6,7-dihydropteridine reductase / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / identical protein binding / membrane / 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 speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsBai, J. / Yang, J. / Zhou, Y. / Yang, Q.
CitationJournal: Chembiochem / Year: 2015
Title: Altering the regioselectivity of a nitroreductase in the synthesis of arylhydroxylamines by structure-based engineering.
Authors: Bai, J. / Zhou, Y. / Chen, Q. / Yang, Q. / Yang, J.
History
DepositionDec 6, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
E: Oxygen-insensitive NAD(P)H nitroreductase
F: Oxygen-insensitive NAD(P)H nitroreductase
G: Oxygen-insensitive NAD(P)H nitroreductase
H: Oxygen-insensitive NAD(P)H nitroreductase
I: Oxygen-insensitive NAD(P)H nitroreductase
J: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,89020
Polymers261,32610
Non-polymers4,56310
Water1086
1
A: Oxygen-insensitive NAD(P)H nitroreductase
B: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1784
Polymers52,2652
Non-polymers9132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-50 kcal/mol
Surface area17380 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)53,1784
Polymers52,2652
Non-polymers9132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-49 kcal/mol
Surface area17030 Å2
MethodPISA
3
E: Oxygen-insensitive NAD(P)H nitroreductase
F: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1784
Polymers52,2652
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-50 kcal/mol
Surface area17110 Å2
MethodPISA
4
G: Oxygen-insensitive NAD(P)H nitroreductase
H: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1784
Polymers52,2652
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-45 kcal/mol
Surface area17240 Å2
MethodPISA
5
I: Oxygen-insensitive NAD(P)H nitroreductase
J: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1784
Polymers52,2652
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-49 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.410, 59.924, 220.063
Angle α, β, γ (deg.)90.00, 99.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxygen-insensitive NAD(P)H nitroreductase / Dihydropteridine reductase / FMN-dependent nitroreductase


Mass: 26132.615 Da / Num. of mol.: 10 / Mutation: T41L, N71S, F124W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: nfnB, dprA, nfsB, nfsI, ntr / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / References: UniProt: P38489, 6,7-dihydropteridine reductase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate, 2%(v/v) Tacsimate, 16%(w/v) Polyethylene glycol 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2014
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 49053 / Num. obs: 48758 / % possible obs: 99.4 % / Redundancy: 3.5 %
Reflection shellResolution: 3→3.05 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DS7

1ds7


Resolution: 3.002→34.863 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1994 4.11 %random
Rwork0.2102 ---
obs0.212 48503 97.55 %-
all-49053 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.51 Å2 / Biso mean: 52.2573 Å2 / Biso min: 39.9 Å2
Refinement stepCycle: LAST / Resolution: 3.002→34.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16860 0 310 6 17176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717550
X-RAY DIFFRACTIONf_angle_d1.12723830
X-RAY DIFFRACTIONf_chiral_restr0.0452660
X-RAY DIFFRACTIONf_plane_restr0.0113010
X-RAY DIFFRACTIONf_dihedral_angle_d15.9446300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0022-3.07730.28411170.27942621273879
3.0773-3.16040.34211480.276933603508100
3.1604-3.25340.30281440.264733293473100
3.2534-3.35830.34241320.258733933525100
3.3583-3.47820.29741530.24843368352199
3.4782-3.61730.27431460.23263341348799
3.6173-3.78180.24521420.22613385352799
3.7818-3.98090.28151400.21343395353599
3.9809-4.22990.24991490.18783346349599
4.2299-4.55590.23491450.18283360350599
4.5559-5.01310.20541450.18163392353799
5.0131-5.73580.24821490.197633873536100
5.7358-7.21590.2411470.200534473594100
7.2159-34.86570.2021370.16653385352294
Refinement TLS params.Method: refined / Origin x: 14.6055 Å / Origin y: 34.2828 Å / Origin z: 54.1853 Å
111213212223313233
T0.4395 Å2-0.0047 Å20.0017 Å2-0.4006 Å20.0033 Å2--0.431 Å2
L0.1289 °2-0.0138 °20.0026 °2-0.0322 °2-0.0053 °2--0.0322 °2
S-0.0045 Å °-0.0095 Å °0.0214 Å °-0.0061 Å °-0.0135 Å °-0.0037 Å °0.0216 Å °0.0046 Å °0.0176 Å °
Refinement TLS groupSelection details: ALL

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