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- PDB-3sxq: Structure of a hexameric multiheme c nitrite reductase from the e... -

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Basic information

Entry
Database: PDB / ID: 3sxq
TitleStructure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio paradoxus
ComponentsEight-heme nitrite reductase
KeywordsOXIDOREDUCTASE / eight hemes c / nitrite reductase
Function / homology
Function and homology information


nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / : / periplasmic space / metal ion binding
Similarity search - Function
Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Up-down Bundle ...Helix Hairpins - #3080 / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / 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 reductase (cytochrome; ammonia-forming)
Similarity search - Component
Biological speciesThioalkalivibrio paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPolyakov, K.M. / Trofimov, A.A. / Tikhonova, T.V. / Tikhonov, A.V. / Boyko, K.M. / Popov, V.O.
CitationJournal: Febs J. / Year: 2012
Title: Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species.
Authors: Tikhonova, T. / Tikhonov, A. / Trofimov, A. / Polyakov, K. / Boyko, K. / Cherkashin, E. / Rakitina, T. / Sorokin, D. / Popov, V.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_special_symmetry ...pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_conn
Revision 1.3Sep 13, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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)129,90840
Polymers118,4582
Non-polymers11,45038
Water23,1311284
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)389,723120
Polymers355,3746
Non-polymers34,349114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area98960 Å2
ΔGint-1674 kcal/mol
Surface area94990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.640, 193.640, 193.640
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-538-

HOH

21A-582-

HOH

31A-594-

HOH

41A-609-

HOH

51A-642-

HOH

61A-646-

HOH

71A-1177-

HOH

81B-537-

HOH

91B-564-

HOH

101B-603-

HOH

111B-631-

HOH

121B-690-

HOH

131B-1000-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Eight-heme nitrite reductase


Mass: 59228.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thioalkalivibrio paradoxus (bacteria) / Strain: ARh1 / References: UniProt: E7EDQ7

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Non-polymers , 8 types, 1322 molecules

#2: Chemical
ChemComp-HEC / 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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1284 / 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: 5.11 Å3/Da / Density % sol: 75.92 %
Crystal growTemperature: 278 K / Method: free-interface-diffusion technique / pH: 6.5
Details: 14 mg/mL protein, 0.02M cobalt chloride, 0.1M MES (pH 6.5), 2.8 M ammonium sulfate, free-interface-diffusion technique, temperature 278.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.9→29.9 Å / Num. all: 188857 / Num. obs: 186813 / % possible obs: 98.9 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.47
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.24 / Num. unique all: 26633 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OT4

2ot4


Resolution: 1.9→29.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.503 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16205 9466 5.1 %RANDOM
Rwork0.1382 ---
obs0.1394 177340 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.556 Å2
Refine analyzeLuzzati coordinate error obs: 0.147 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8181 0 766 1284 10231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0219411
X-RAY DIFFRACTIONr_angle_refined_deg1.4932.14712891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31151034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35123.586449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.712151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5061563
X-RAY DIFFRACTIONr_chiral_restr0.1080.21205
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217403
X-RAY DIFFRACTIONr_mcbond_it0.4871.2389
X-RAY DIFFRACTIONr_mcangle_it0.91.5638
X-RAY DIFFRACTIONr_scbond_it0.7251.5249
X-RAY DIFFRACTIONr_scangle_it1.1972217
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 699 -
Rwork0.182 13149 -
obs--99.71 %

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