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

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Basic information

Entry
Database: PDB / ID: 8rxu
TitleCrystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in space group P21
ComponentsOctaheme nitrite reductase
KeywordsOXIDOREDUCTASE / octaheme nitrite reductase / wild type
Function / homologyHEME C / PHOSPHATE ION
Function and homology information
Biological speciesTrichlorobacter ammonificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.737 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 space group P21
Authors: Polyakov, K.M. / Safonova, T.N. / Osipov, E. / Popov, A.N. / Tikhonova, T.V. / Popov, V.O.
History
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Octaheme nitrite reductase
MMM: Octaheme nitrite reductase
YYY: Octaheme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,72833
Polymers166,4793
Non-polymers15,24930
Water17,114950
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37500 Å2
ΔGint-628 kcal/mol
Surface area53900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.200, 64.800, 114.200
Angle α, β, γ (deg.)90.000, 119.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Octaheme nitrite reductase


Mass: 55493.074 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trichlorobacter ammonificans (bacteria)
#2: Chemical...
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 17-20 % PEG 3350, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.4003
pseudo-merohedral22L, K, -H-L20.2901
pseudo-merohedral33-H-L, K, H30.3097
ReflectionResolution: 1.737→42.877 Å / Num. obs: 145919 / % possible obs: 98 % / Redundancy: 4.2 % / CC1/2: 0.996 / Net I/σ(I): 10.7
Reflection shellResolution: 1.737→1.83 Å / Rmerge(I) obs: 0.956 / Num. unique obs: 101804 / CC1/2: 0.844

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.737→42.877 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.262 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2542 7348 5.036 %
Rwork0.1913 138571 -
all0.195 --
obs-145919 97.76 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.354 Å2
Baniso -1Baniso -2Baniso -3
1--2.737 Å2-0 Å25.607 Å2
2--9.76 Å20 Å2
3----7.023 Å2
Refinement stepCycle: LAST / Resolution: 1.737→42.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11665 0 1050 950 13665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01413281
X-RAY DIFFRACTIONr_bond_other_d0.0020.01811720
X-RAY DIFFRACTIONr_angle_refined_deg3.0561.80818260
X-RAY DIFFRACTIONr_angle_other_deg1.4451.67527242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.49451484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52522.812626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.199152127
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.447153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8831563
X-RAY DIFFRACTIONr_chiral_restr0.1720.21572
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0214902
X-RAY DIFFRACTIONr_gen_planes_other0.0150.022785
X-RAY DIFFRACTIONr_nbd_refined0.2130.23838
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.213696
X-RAY DIFFRACTIONr_nbtor_refined0.1690.25918
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.26027
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2855
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0980.215
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.218
X-RAY DIFFRACTIONr_nbd_other0.2120.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.216
X-RAY DIFFRACTIONr_mcbond_it2.1812.2755939
X-RAY DIFFRACTIONr_mcbond_other2.1812.2755938
X-RAY DIFFRACTIONr_mcangle_it2.8933.4127419
X-RAY DIFFRACTIONr_mcangle_other2.8933.4127420
X-RAY DIFFRACTIONr_scbond_it1.972.2777342
X-RAY DIFFRACTIONr_scbond_other1.9692.2777328
X-RAY DIFFRACTIONr_scangle_it2.6033.37510840
X-RAY DIFFRACTIONr_scangle_other2.6013.37510822
X-RAY DIFFRACTIONr_lrange_it3.97626.05617009
X-RAY DIFFRACTIONr_lrange_other3.95126.02716896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.737-1.7820.6016120.4739410X-RAY DIFFRACTION91.2501
1.782-1.8310.454790.3159715X-RAY DIFFRACTION95.6106
1.831-1.8840.3774910.2719809X-RAY DIFFRACTION99.1242
1.884-1.9420.3154630.2249608X-RAY DIFFRACTION98.9973
1.942-2.0060.3094150.2299291X-RAY DIFFRACTION99.0105
2.006-2.0760.2854440.2218856X-RAY DIFFRACTION97.9463
2.076-2.1550.2834490.2128569X-RAY DIFFRACTION98.1498
2.155-2.2430.2834660.2048116X-RAY DIFFRACTION97.756
2.243-2.3420.264520.1857754X-RAY DIFFRACTION96.7346
2.342-2.4570.2444700.1847556X-RAY DIFFRACTION99.7142
2.457-2.5890.2473200.1837409X-RAY DIFFRACTION99.6647
2.589-2.7460.2483440.1866923X-RAY DIFFRACTION99.5616
2.746-2.9360.2773400.1876449X-RAY DIFFRACTION98.4627
2.936-3.1710.2323610.1895811X-RAY DIFFRACTION97.4885
3.171-3.4730.2642880.195462X-RAY DIFFRACTION96.428
3.473-3.8820.1883440.1594955X-RAY DIFFRACTION99.8681
3.882-4.4820.1851870.1294524X-RAY DIFFRACTION99.7882
4.482-5.4860.1812120.1443825X-RAY DIFFRACTION99.5316
5.486-7.7470.1891570.1642813X-RAY DIFFRACTION94.7368
7.747-42.8770.204540.1581716X-RAY DIFFRACTION98.5523

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