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- PDB-6fwf: Low resolution structure of Neisseria meningitidis qNOR -

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Basic information

Entry
Database: PDB / ID: 6fwf
TitleLow resolution structure of Neisseria meningitidis qNOR
ComponentsNitric-oxide reductase
KeywordsOXIDOREDUCTASE / reductase / membrane-bound / nitric oxide
Function / homology
Function and homology information


nitric-oxide reductase / cytochrome-c oxidase activity / aerobic respiration / heme binding / metal ion binding / membrane
Similarity search - Function
: / Nitric oxide reductase subunit B, cytochrome c-like domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Nitric-oxide reductase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsYoung, D. / Antonyuk, S. / Tosha, T. / Hisano, T. / Hasnain, S. / Shiro, Y.
CitationJournal: Sci Rep / Year: 2018
Title: Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme.
Authors: Gonska, N. / Young, D. / Yuki, R. / Okamoto, T. / Hisano, T. / Antonyuk, S. / Hasnain, S.S. / Muramoto, K. / Shiro, Y. / Tosha, T. / Adelroth, P.
History
DepositionMar 6, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMar 14, 2018ID: 6ELH
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitric-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7185
Polymers84,3891
Non-polymers1,3294
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-73 kcal/mol
Surface area31380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.682, 123.096, 130.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nitric-oxide reductase


Mass: 84389.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (strain alpha14) (bacteria)
Strain: alpha14 / Gene: norB, NMO_1451 / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43(DE3) / References: UniProt: C6S880, nitric-oxide reductase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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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: 4.47 Å3/Da / Density % sol: 72.48 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 400, cadmium chloride, magnesium chloride, 2-(N-morpholino)ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.2→53.64 Å / Num. obs: 11511 / % possible obs: 99.86 % / Redundancy: 14.4 % / Biso Wilson estimate: 170.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.07 / Rrim(I) all: 0.261 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.2-4.714.97.68132180.2642.0537.95499.9
9.39-53.6412.20.06911210.9980.0210.07399.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AYF

3ayf


Resolution: 4.2→53.64 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.82 / SU B: 137.639 / SU ML: 1.627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3734 509 4.4 %RANDOM
Rwork0.3333 ---
obs0.335 11004 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 616.17 Å2 / Biso mean: 287.437 Å2 / Biso min: 99.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.75 Å20 Å2-0 Å2
2---5.94 Å20 Å2
3----1.81 Å2
Refinement stepCycle: final / Resolution: 4.2→53.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 0 88 0 5762
Biso mean--248.5 --
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025965
X-RAY DIFFRACTIONr_bond_other_d0.0020.025423
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9528130
X-RAY DIFFRACTIONr_angle_other_deg1.043312458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1775703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81323.202253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4515882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.921520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026606
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021412
LS refinement shellResolution: 4.2→4.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.503 35 -
Rwork0.499 807 -
all-842 -
obs--99.76 %

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