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- PDB-7dp1: Crystal structure of FMN and NADPH-dependent nitroreductase NfnB ... -

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Basic information

Entry
Database: PDB / ID: 7dp1
TitleCrystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88A derived from sphigopyxis sp. strain HMH
ComponentsNitroreductase family protein
KeywordsOXIDOREDUCTASE / dinitroaniline herbicides reductase
Function / homologyNitroreductase / Nitroreductase family / Nitroreductase-like / oxidoreductase activity / nucleotide binding / FLAVIN MONONUCLEOTIDE / Nitroreductase family protein
Function and homology information
Biological speciesSphingopyxis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00349582522 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)52,3574
Polymers51,4442
Non-polymers9132
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-56 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.825, 90.825, 102.225
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
11LEULEUTYRTYRchain 'A'AA9 - 1089 - 108
12ALAALAPHEPHEchain 'A'AA119 - 231119 - 231
23LEULEUTYRTYRchain 'B'BB9 - 1089 - 108
24ALAALAPHEPHEchain 'B'BB119 - 231119 - 231

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Components

#1: Protein Nitroreductase family protein / nitroreductase / NfnB


Mass: 25722.197 Da / Num. of mol.: 2 / Mutation: Y88A
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


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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH7.0, 40% PEG300, 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: 0.97934 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: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29391 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 36.9420219667 Å2 / CC1/2: 0.996 / Net I/σ(I): 19.44
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 2867 / CC1/2: 0.537

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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: 2.00349582522→31.9036119211 Å / SU ML: 0.279365551014 / Cross valid method: FREE R-VALUE / σ(F): 1.33784634817 / Phase error: 26.417308092
RfactorNum. reflection% reflection
Rfree0.256964955106 1998 6.81283458929 %
Rwork0.199787080119 27329 -
obs0.20364580849 29327 99.8807983107 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.0660482769 Å2
Refinement stepCycle: LAST / Resolution: 2.00349582522→31.9036119211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 62 57 3486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008351324354413519
X-RAY DIFFRACTIONf_angle_d1.210513941824790
X-RAY DIFFRACTIONf_chiral_restr0.0495308774919494
X-RAY DIFFRACTIONf_plane_restr0.00674398252186625
X-RAY DIFFRACTIONf_dihedral_angle_d15.91566592351266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0035-2.05360.3681728796341380.3127940464031885X-RAY DIFFRACTION99.2639842983
2.0536-2.10910.3220321680171410.3064033139441927X-RAY DIFFRACTION99.9516674722
2.1091-2.17120.3708749366231400.2812248658461917X-RAY DIFFRACTION100
2.1712-2.24120.2863496098231400.261111362071920X-RAY DIFFRACTION100
2.2412-2.32130.291738409911410.2488961352661921X-RAY DIFFRACTION100
2.3213-2.41420.3137740895841410.2379523959621934X-RAY DIFFRACTION100
2.4142-2.5240.2799854153391430.2378409621971938X-RAY DIFFRACTION100
2.524-2.6570.2548888518861400.2154888013531924X-RAY DIFFRACTION100
2.657-2.82340.2754418364531420.2079928530331944X-RAY DIFFRACTION99.9520843316
2.8234-3.04130.2527073722631440.1887229861311959X-RAY DIFFRACTION100
3.0413-3.3470.2617850393151430.1997007862531963X-RAY DIFFRACTION99.9525391552
3.347-3.83070.2067689428461440.1764222820651973X-RAY DIFFRACTION100
3.8307-4.82350.2343512581151480.1639300221852011X-RAY DIFFRACTION100
4.8235-31.90.2480218981651530.1830974002522113X-RAY DIFFRACTION99.2988606486
Refinement TLS params.Method: refined / Origin x: 17.6505946731 Å / Origin y: -18.338131681 Å / Origin z: -0.180391456691 Å
111213212223313233
T0.207135960232 Å2-0.00148362669834 Å2-0.00566310943058 Å2-0.218781877999 Å2-0.0107764967947 Å2--0.228521489175 Å2
L2.40733626587 °20.504425117506 °2-0.481121867466 °2-3.53999276713 °2-1.49352018941 °2--4.24051435334 °2
S0.0927976915164 Å °-0.123643073835 Å °0.0594958602104 Å °0.0822728219886 Å °-0.0298480784975 Å °-0.0115928915821 Å °-0.195002965483 Å °0.147801196108 Å °-0.0534280297357 Å °
Refinement TLS groupSelection details: all

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