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- PDB-8rv0: Crystal structure of octaheme nitrite reductase from Trichlorobac... -

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Basic information

Entry
Database: PDB / ID: 8rv0
TitleCrystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in complex with nitrite
ComponentsOctaheme cytochrome c nitrite reductase
KeywordsOXIDOREDUCTASE / Octaheme nitrite reductase / complex with nitrite
Function / homologyHEME C / NITRIC OXIDE / NITRITE ION
Function and homology information
Biological speciesTrichlorobacter ammonificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPolyakov, K.M. / Safonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-74-30004 Russian Federation
CitationJournal: To Be Published
Title: Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in complex with nitrite
Authors: Polyakov, K.M. / Safonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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
Y: Octaheme cytochrome c nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,55712
Polymers55,4931
Non-polymers5,06411
Water8,107450
1
Y: Octaheme cytochrome c nitrite reductase
hetero molecules

Y: Octaheme cytochrome c nitrite reductase
hetero molecules

Y: Octaheme cytochrome c nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,67236
Polymers166,4793
Non-polymers15,19233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area38130 Å2
ΔGint-598 kcal/mol
Surface area53990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.440, 114.440, 65.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11Y-1066-

HOH

21Y-1126-

HOH

31Y-1137-

HOH

41Y-1145-

HOH

51Y-1148-

HOH

61Y-1150-

HOH

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Components

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Protein , 1 types, 1 molecules Y

#1: Protein Octaheme cytochrome c nitrite reductase


Mass: 55493.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichlorobacter ammonificans (bacteria)

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Non-polymers , 5 types, 461 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 mM NaNO2, 0.1 M Bis-Tris, pH 5.7, 17-20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Sep 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.55→49.6 Å / Num. obs: 69684 / % possible obs: 0.988 % / Redundancy: 4.4 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 1.55→1.59 Å / Num. unique obs: 5157 / CC1/2: 0.788

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→49.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.768 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25495 3361 4.8 %RANDOM
Rwork0.20316 ---
obs0.20558 66322 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.31 Å2-0 Å2
2---0.63 Å20 Å2
3---2.03 Å2
Refinement stepCycle: 1 / Resolution: 1.55→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 350 450 4691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0134439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.4211.8036097
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6735494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71522.891211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97815716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.651521
X-RAY DIFFRACTIONr_chiral_restr0.2270.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.023461
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4442.3811980
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3143.5582472
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.092.4372459
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.58232.1177517
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 318 -
Rwork0.354 4838 -
obs--99.52 %

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