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- PDB-7dp2: Crystal structure of FMN and NADPH-dependent nitroreductase NfnB ... -

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Basic information

Entry
Database: PDB / ID: 7dp2
TitleCrystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH
ComponentsNitroreductase family protein
KeywordsOXIDOREDUCTASE / dinitroaniline herbicides reductase
Function / homologyNitroreductase / Nitroreductase family / Nitroreductase-like / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / Nitroreductase family protein
Function and homology information
Biological speciesSphingopyxis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40008728899 Å
AuthorsKim, S.H. / Park, S. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A4A1018890 Korea, Republic Of
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structure and substrate specificity determinants of NfnB, a dinitroaniline herbicide-catabolizing nitroreductase from Sphingopyxis sp. strain HMH.
Authors: Kim, S.H. / Park, S. / Park, E. / Kim, J.H. / Ghatge, S. / Hur, H.G. / Rhee, S.
History
DepositionDec 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitroreductase family protein
B: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5094
Polymers51,5972
Non-polymers9132
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-58 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.436, 90.436, 101.679
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUILEILEchain 'A'AA9 - 1139 - 113
12GLYGLYPHEPHEchain 'A'AA120 - 231120 - 231
23LEULEUILEILEchain 'B'BB9 - 1139 - 113
24GLYGLYPHEPHEchain 'B'BB120 - 231120 - 231

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Components

#1: Protein Nitroreductase family protein / nitroreductase / NfnB


Mass: 25798.293 Da / Num. of mol.: 2 / Mutation: Y88F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2L0VUJ4
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH7.0, 40% PEG 300, 8% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 17096 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 57.6956791201 Å2 / CC1/2: 0.994 / Net I/σ(I): 20.2
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 1665 / CC1/2: 0.454

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WZW

2wzw


Resolution: 2.40008728899→33.7873329824 Å / SU ML: 0.344100466426 / Cross valid method: FREE R-VALUE / σ(F): 1.336822377 / Phase error: 26.1153362806
RfactorNum. reflection% reflection
Rfree0.256843483919 1704 10 %
Rwork0.185265108183 15336 -
obs0.192250261313 17040 99.818405483 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.5171893671 Å2
Refinement stepCycle: LAST / Resolution: 2.40008728899→33.7873329824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 62 9 3520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008659189255853604
X-RAY DIFFRACTIONf_angle_d1.272500277294905
X-RAY DIFFRACTIONf_chiral_restr0.055258118378505
X-RAY DIFFRACTIONf_plane_restr0.00646883886198641
X-RAY DIFFRACTIONf_dihedral_angle_d17.18341234621297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.47070.4004549810931380.300816424911233X-RAY DIFFRACTION98.4913793103
2.4707-2.55040.3303894367351380.2692719485031246X-RAY DIFFRACTION100
2.5504-2.64150.30892328241380.239103393361246X-RAY DIFFRACTION100
2.6415-2.74720.3301679477631410.2329027932451263X-RAY DIFFRACTION100
2.7472-2.87220.3141944413061390.214531459671258X-RAY DIFFRACTION100
2.8722-3.02360.2444602064821420.1909929187631277X-RAY DIFFRACTION100
3.0236-3.21290.2826356168191400.1942657500841261X-RAY DIFFRACTION100
3.2129-3.46070.2530853732721410.191034500231269X-RAY DIFFRACTION100
3.4607-3.80850.2424958385871430.1712402805831285X-RAY DIFFRACTION100
3.8085-4.35860.2211226203551430.1632670409141290X-RAY DIFFRACTION100
4.3586-5.48760.2236944936251470.1700846408941317X-RAY DIFFRACTION99.9317406143
5.4876-33.780.2642053275281540.1742818576781391X-RAY DIFFRACTION99.4208494208
Refinement TLS params.Method: refined / Origin x: 17.9483803954 Å / Origin y: 72.7353309799 Å / Origin z: 0.1418559476 Å
111213212223313233
T0.350553716521 Å20.0142685373841 Å2-0.0509979309526 Å2-0.350959008763 Å2-0.0115236549177 Å2--0.374504322201 Å2
L5.19841066397 °20.624426894703 °2-1.89579782404 °2-2.87616538772 °2-0.771726161557 °2--4.09520709679 °2
S0.100634639163 Å °0.17952307459 Å °-0.0197857299569 Å °-0.139302568896 Å °0.0791182964432 Å °0.0987923649881 Å °0.0473835266772 Å °-0.197676776903 Å °-0.143611519218 Å °
Refinement TLS groupSelection details: all

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