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- PDB-3d1i: Structure of the Thioalkalivibrio nitratireducens cytochrome c ni... -

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Basic information

Entry
Database: PDB / ID: 3d1i
TitleStructure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / cytochrome C nitrite reductase / NRFA / Sulfite reductase
Function / homology
Function and homology information


ammonium ion metabolic process / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded periplasmic space / periplasmic space / calcium ion binding / heme binding
Similarity search - Function
Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins ...Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / NITRITE ION / Chem-PG6 / Cytochrome c-552 / Cytochrome c-552
Similarity search - Component
Biological speciesThioalkalivibrio nitratireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPolyakov, K.M. / Boyko, K.M. / Slutsky, A. / Tikhonova, T.V. / Antipov, A.N. / Zvyagilskaya, R.A. / Popov, A.N. / Lamzin, V.S. / Bourenkov, G.P. / Popov, V.O.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens
Authors: Polyakov, K.M. / Boyko, K.M. / Tikhonova, T.V. / Slutsky, A. / Antipov, A.N. / Zvyagilskaya, R.A. / Popov, A.N. / Bourenkov, G.P. / Lamzin, V.S. / Popov, V.O.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray analysis of cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens
Authors: Boyko, K.M. / Polyakov, K.M. / Tikhonova, T.V. / Slutsky, A. / Antipov, A.N. / Zvyagilskaya, R.A. / Bourenkov, G.P. / Popov, A.N. / Lamzin, V.S. / Popov, V.O.
#2: Journal: Biochim.Biophys.Acta / Year: 2006
Title: Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens
Authors: Tikhonova, T.V. / Slutsky, A. / Antipov, A.N. / Boyko, K.M. / Polyakov, K.M. / Sorokin, D.Y. / Zvyagilskaya, R.A. / Popov, V.O.
History
DepositionMay 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,87534
Polymers118,9832
Non-polymers11,89232
Water20,3571130
1
A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules

A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules

A: Eight-heme nitrite reductase
B: Eight-heme nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,625102
Polymers356,9486
Non-polymers35,67796
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area96180 Å2
ΔGint-1158.6 kcal/mol
Surface area94110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.412, 193.412, 193.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-529-

NA

21B-529-

NA

31B-1908-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Eight-heme nitrite reductase


Mass: 59491.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio nitratireducens (bacteria)
Strain: ALEN 2 / References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS

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Non-polymers , 7 types, 1162 molecules

#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1130 / Source method: isolated from a natural source / Formula: H2O

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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: 5.07 Å3/Da / Density % sol: 75.73 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: The drop contained 5ml of enzyme solution (14.5mg/ml) in 0.005M Tris-borat buffer (PH8.7) and 5ml reservoir solution. The reservoir solution contained 27% PEG400, 0.18M sodium citrate in 0. ...Details: The drop contained 5ml of enzyme solution (14.5mg/ml) in 0.005M Tris-borat buffer (PH8.7) and 5ml reservoir solution. The reservoir solution contained 27% PEG400, 0.18M sodium citrate in 0.09M Tris buffer (PH8.5), complex with nitrite ion was obtained by soaking crystal in reservoir solution with 100mM sodium nitrite by 30 minute, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 1.8→13 Å / Num. obs: 228600 / % possible obs: 99.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.82 Å / Rmerge(I) obs: 0.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OT4

2ot4


Resolution: 1.8→11.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.371 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16547 11051 5 %RANDOM
Rwork0.1485 ---
obs0.14936 208802 99.47 %-
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: 16.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.155 Å / Luzzati sigma a obs: 0.029 Å
Refinement stepCycle: LAST / Resolution: 1.8→11.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8225 0 767 1130 10122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0219520
X-RAY DIFFRACTIONr_bond_other_d0.0020.025816
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.14412990
X-RAY DIFFRACTIONr_angle_other_deg1.049314033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12751036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36723.704467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.419151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0291567
X-RAY DIFFRACTIONr_chiral_restr0.1140.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0210627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021916
X-RAY DIFFRACTIONr_nbd_refined0.2230.22329
X-RAY DIFFRACTIONr_nbd_other0.2150.27209
X-RAY DIFFRACTIONr_nbtor_refined0.190.24696
X-RAY DIFFRACTIONr_nbtor_other0.0940.24548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2994
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.2148
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.282
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0950.24
X-RAY DIFFRACTIONr_mcbond_it0.8411.55185
X-RAY DIFFRACTIONr_mcbond_other0.2711.52083
X-RAY DIFFRACTIONr_mcangle_it1.40828345
X-RAY DIFFRACTIONr_scbond_it2.23834759
X-RAY DIFFRACTIONr_scangle_it3.3684.54644
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 778 -
Rwork0.234 15352 -
obs--99.26 %

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