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- PDB-6tsi: cd1 nitrite reductase NirS with bound dihydro-heme d1 -

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Basic information

Entry
Database: PDB / ID: 6tsi
Titlecd1 nitrite reductase NirS with bound dihydro-heme d1
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / cd1 nitrite reductase / NirS
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome D1 heme domain / : / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME D / HEME C / PHOSPHATE ION / Nitrite reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.38 Å
AuthorsKluenemann, T. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2223/1 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structure of heme d 1 -free cd 1 nitrite reductase NirS.
Authors: Klunemann, T. / Blankenfeldt, W.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrite reductase
B: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,83216
Polymers120,5182
Non-polymers3,31414
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13830 Å2
ΔGint-197 kcal/mol
Surface area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.762, 91.093, 112.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11B-823-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nitrite reductase / Cytochrome cd1 / Cytochrome oxidase / Hydroxylamine reductase


Mass: 60259.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria)
References: UniProt: P24474, nitrite reductase (NO-forming), hydroxylamine reductase

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Non-polymers , 5 types, 260 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-DHE / HEME D


Mass: 712.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.49 Å3/Da / Density % sol: 64.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.9M K2HPO4 0.1M Tris-HCl pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.7389 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7389 Å / Relative weight: 1
ReflectionResolution: 2.38→112.71 Å / Num. obs: 50095 / % possible obs: 92.6 % / Redundancy: 12.5 % / CC1/2: 0.99 / Rpim(I) all: 0.11 / Net I/σ(I): 6.6
Reflection shellResolution: 2.38→2.62 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2505 / CC1/2: 0.64 / Rpim(I) all: 0.54 / % possible all: 44.5

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Processing

Software
NameVersionClassification
PHENIX1.18rc1-3769refinement
XDSdata reduction
autoPROCdata collection
STARANISOdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1nir

1nir


Resolution: 2.38→79.61 Å / SU ML: 0.2594 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.0379
RfactorNum. reflection% reflection
Rfree0.2795 2513 5.02 %
Rwork0.2379 --
obs0.24 50038 72.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.61 Å2
Refinement stepCycle: LAST / Resolution: 2.38→79.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8364 0 214 246 8824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00968806
X-RAY DIFFRACTIONf_angle_d1.369912053
X-RAY DIFFRACTIONf_chiral_restr0.0791286
X-RAY DIFFRACTIONf_plane_restr0.00411551
X-RAY DIFFRACTIONf_dihedral_angle_d17.32793213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.420.4305100.3259181X-RAY DIFFRACTION5.13
2.42-2.470.3364140.3437283X-RAY DIFFRACTION7.88
2.47-2.520.5176160.318425X-RAY DIFFRACTION11.72
2.52-2.580.3871450.3309733X-RAY DIFFRACTION20.86
2.58-2.650.3848690.34251453X-RAY DIFFRACTION40.26
2.65-2.720.29821170.32782200X-RAY DIFFRACTION61.49
2.72-2.80.32911510.32322756X-RAY DIFFRACTION77.01
2.8-2.890.31761610.3123167X-RAY DIFFRACTION87.56
2.89-2.990.3681800.29863418X-RAY DIFFRACTION95.59
2.99-3.110.31281970.28763579X-RAY DIFFRACTION99.39
3.11-3.250.331660.27443642X-RAY DIFFRACTION99.97
3.25-3.430.29082000.22913610X-RAY DIFFRACTION100
3.43-3.640.27332050.21013615X-RAY DIFFRACTION99.92
3.64-3.920.22391860.19853626X-RAY DIFFRACTION99.97
3.92-4.320.25372020.18343638X-RAY DIFFRACTION99.92
4.32-4.940.19691930.17323667X-RAY DIFFRACTION100
4.94-6.220.26481910.21673707X-RAY DIFFRACTION99.87
6.23-79.610.27242100.24683825X-RAY DIFFRACTION98.8

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